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macros.xml
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macros.xml
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<macros>
<xml name="requirements">
<requirements>
<requirement type="package" version="3.9">python</requirement>
<requirement type="package" version="1.81">biopython</requirement>
<requirement type="package" version="1.2.2">cpt_gffparser</requirement>
<yield/>
</requirements>
</xml>
<token name="@WRAPPER_VERSION@">2.4.0</token>
<xml name="citation/gepard">
<citation type="doi">10.1093/bioinformatics/btm039</citation>
</xml>
<token name="@XMFA_INPUT@">
'$xmfa'
</token>
<xml name="xmfa_input" token_formats="xmfa">
<param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
</xml>
<token name="@XMFA_FA_INPUT@">
'$sequences'
</token>
<xml name="xmfa_fa_input">
<param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
</xml>
<xml name="genome_selector">
<conditional name="reference_genome">
<param name="reference_genome_source" type="select" label="Reference Genome">
<option value="history" selected="True">From History</option>
<option value="cached">Locally Cached</option>
</param>
<when value="cached">
<param name="fasta_indexes" type="select" label="Source FASTA Sequence">
<options from_data_table="all_fasta"/>
</param>
</when>
<when value="history">
<param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
</when>
</conditional>
</xml>
<xml name="gff3_input">
<param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
</xml>
<xml name="input/gff3+fasta">
<expand macro="gff3_input"/>
<expand macro="genome_selector"/>
</xml>
<xml name="citation/mijalisrasche">
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">@unpublished{galaxyTools,
author = {E. Mijalis, H. Rasche},
title = {CPT Galaxy Tools},
year = {2013-2017},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {E. Mijalis, H. Rasche},
title = {CPT Galaxy Tools},
year = {2013-2017},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</citations>
</xml>
<xml name="citations-crr">
<citations>
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {C. Ross},
title = {CPT Galaxy Tools},
year = {2020-},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</citations>
</xml>
<xml name="citations-2020">
<citations>
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {E. Mijalis, H. Rasche},
title = {CPT Galaxy Tools},
year = {2013-2017},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {A. Criscione},
title = {CPT Galaxy Tools},
year = {2019-2021},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</citations>
</xml>
<xml name="citations-2020-AJC-solo">
<citations>
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {A. Criscione},
title = {CPT Galaxy Tools},
year = {2019-2021},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</citations>
</xml>
<xml name="citations-clm">
<citations>
<citation type="doi">10.1371/journal.pcbi.1008214</citation>
<citation type="bibtex">
@unpublished{galaxyTools,
author = {C. Maughmer},
title = {CPT Galaxy Tools},
year = {2017-2020},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</citations>
</xml>
<xml name="sl-citations-clm">
<citation type="bibtex">
@unpublished{galaxyTools,
author = {C. Maughmer},
title = {CPT Galaxy Tools},
year = {2017-2020},
note = {https://github.com/tamu-cpt/galaxy-tools/}
}
</citation>
<yield/>
</xml>
<token name="@INPUT_GFF@">
'$gff3_data'
</token>
<token name="@INPUT_FASTA@">
#if str($reference_genome.reference_genome_source) == 'cached':
'${reference_genome.fasta_indexes.fields.path}'
#else if str($reference_genome.reference_genome_source) == 'history':
genomeref.fa
#end if
</token>
<token name="@GENOME_SELECTOR_PRE@">
#if $reference_genome.reference_genome_source == 'history':
ln -s '$reference_genome.genome_fasta' genomeref.fa;
#end if
</token>
<token name="@GENOME_SELECTOR@">
#if str($reference_genome.reference_genome_source) == 'cached':
'${reference_genome.fasta_indexes.fields.path}'
#else if str($reference_genome.reference_genome_source) == 'history':
genomeref.fa
#end if
</token>
</macros>