diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
index 9771fe8a1..df831a515 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
@@ -1,5 +1,11 @@
# Changelog
+## [0.5] 2024-09-25
+
+### Manual update
+- `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`
+
## [0.4] 2024-04-08
### Automatic update
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
index eb13dcea9..723587f8b 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
@@ -54,15 +54,11 @@
Number of expected cells: 500
outputs:
MultiQC_STARsolo:
- class: File
asserts:
- - that: "has_text_matching"
- expression: ">subsample3[0-9].[0-9]% | | "
Seurat input for gene expression (filtered):
- class: Collection
- collection_type: list:list
+ attributes: { collection_type: list:list }
element_tests:
subsample:
elements:
@@ -79,8 +75,7 @@
has_line:
line: "FBgn0250732 gfzf"
CITE-seq-Count report:
- class: Collection
- collection_type: list
+ attributes: { collection_type: list }
element_tests:
subsample:
asserts:
@@ -93,8 +88,7 @@
- that: "has_line"
line: "Percentage unmapped: 1"
Seurat input for CMO (UMI):
- class: Collection
- collection_type: list:list
+ attributes: { collection_type: list:list }
element_tests:
subsample:
elements:
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
index 7ea0d5b76..04abdf111 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
@@ -1,6 +1,7 @@
{
"a_galaxy_workflow": "true",
"annotation": "This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.",
+ "comments": [],
"creator": [
{
"class": "Person",
@@ -30,7 +31,7 @@
],
"format-version": "0.1",
"license": "MIT",
- "release": "0.4",
+ "release": "0.5",
"name": "scRNA-seq_preprocessing_10X_cellPlex",
"steps": {
"0": {
@@ -464,7 +465,7 @@
},
"5": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"errors": null,
"id": 5,
"input_connections": {
@@ -572,15 +573,15 @@
"output_name": "reads_per_gene"
}
},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "42ce70172b72",
+ "changeset_revision": "45795f582ae9",
"name": "rna_starsolo",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.7.11a+galaxy0",
+ "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.7.11a+galaxy1",
"type": "tool",
"uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5",
"when": null,
@@ -588,7 +589,7 @@
},
"6": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
@@ -605,13 +606,13 @@
"label": "multiQC",
"name": "MultiQC",
"outputs": [
- {
- "name": "stats",
- "type": "input"
- },
{
"name": "html_report",
"type": "html"
+ },
+ {
+ "name": "stats",
+ "type": "tabular"
}
],
"position": {
@@ -625,15 +626,15 @@
"output_name": "stats"
}
},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"tool_shed_repository": {
- "changeset_revision": "abfd8a6544d7",
+ "changeset_revision": "f7e2f1eb3a16",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "1.11+galaxy1",
+ "tool_version": "1.24.1+galaxy0",
"type": "tool",
"uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
"when": null,
@@ -954,7 +955,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -999,7 +1000,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1044,7 +1045,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1295,8 +1296,8 @@
]
}
},
- "tags": "",
- "uuid": "89502a02-ec65-400c-b428-68eda7ea6b40"
+ "tags": [],
+ "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a"
},
"tool_id": null,
"type": "subworkflow",
@@ -1311,7 +1312,7 @@
]
}
},
- "tags": "",
+ "tags": [],
"uuid": "a999ad68-faa9-4ccb-81b4-ac648af028bd"
},
"tool_id": null,
@@ -1534,7 +1535,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1753,7 +1754,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1798,7 +1799,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1843,7 +1844,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2094,7 +2095,7 @@
]
}
},
- "tags": "",
+ "tags": [],
"uuid": "79342c4e-bb7a-4b25-a214-7d5a10fbfd79"
},
"tool_id": null,
@@ -2166,6 +2167,6 @@
"tags": [
"#single-cell"
],
- "uuid": "b8bd25f7-caa3-44da-8329-26dce6d46636",
- "version": 4
+ "uuid": "470536e7-ac58-4859-94d6-2085be9c2e17",
+ "version": 3
}
\ No newline at end of file
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
index 82a7c4eee..dcfa61c1d 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
@@ -29,15 +29,11 @@
filetype: tabular
outputs:
'MultiQC on input dataset(s): Webpage':
- class: File
asserts:
- - that: "has_text_matching"
- expression: ">subsample3[0-9].[0-9]% | | "
Seurat input for gene expression (filtered):
- class: Collection
- collection_type: list:list
+ attributes: { collection_type: list:list }
element_tests:
subsample:
elements:
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
index 89f7de368..dd5740b2b 100644
--- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
@@ -30,7 +30,7 @@
],
"format-version": "0.1",
"license": "MIT",
- "release": "0.4",
+ "release": "0.5",
"name": "scRNA-seq_preprocessing_10X_v3_Bundle",
"steps": {
"0": {
@@ -170,7 +170,7 @@
},
"5": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"errors": null,
"id": 5,
"input_connections": {
@@ -278,15 +278,15 @@
"output_name": "reads_per_gene"
}
},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "42ce70172b72",
+ "changeset_revision": "45795f582ae9",
"name": "rna_starsolo",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.7.11a+galaxy0",
+ "tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"RuntimeValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"RuntimeValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"RuntimeValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.7.11a+galaxy1",
"type": "tool",
"uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5",
"when": null,
@@ -294,7 +294,7 @@
},
"6": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
@@ -311,13 +311,13 @@
"label": "multiQC",
"name": "MultiQC",
"outputs": [
- {
- "name": "stats",
- "type": "input"
- },
{
"name": "html_report",
"type": "html"
+ },
+ {
+ "name": "stats",
+ "type": "tabular"
}
],
"position": {
@@ -331,15 +331,15 @@
"output_name": "stats"
}
},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"tool_shed_repository": {
- "changeset_revision": "abfd8a6544d7",
+ "changeset_revision": "f7e2f1eb3a16",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "1.11+galaxy1",
+ "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "1.24.1+galaxy0",
"type": "tool",
"uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
"when": null,
@@ -660,7 +660,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -705,7 +705,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -750,7 +750,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
- "changeset_revision": "fbf99087e067",
+ "changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1001,8 +1001,8 @@
]
}
},
- "tags": "",
- "uuid": "415c1b14-3b63-4d27-8c34-42e452cb49f1"
+ "tags": [],
+ "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a"
},
"tool_id": null,
"type": "subworkflow",
@@ -1020,6 +1020,6 @@
"tags": [
"#single-cell"
],
- "uuid": "19feac09-8db7-4e3f-9774-8b815918cfa7",
+ "uuid": "87f25ddb-a663-4582-9ec6-d0b4bef4109c",
"version": 2
}
\ No newline at end of file