Mercurial > repos > iuc > stacks_stats
view stacks_stats.xml @ 0:fe6be53294c9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author | iuc |
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date | Thu, 27 Apr 2017 04:18:05 -0400 |
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children | 93b16407d6e9 |
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<tool id="stacks_stats" name="Stacks: statistics" version="@WRAPPER_VERSION@.0"> <description>on stacks found for multiple samples</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ mkdir stacks_inputs && #for $input_file in $input_col #set $ext = "" #if not str($input_file.element_identifier).endswith('.tsv') #set $ext = ".tsv" #end if ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' && #end for stacks_summary.py --stacks-prog '$program' --res-dir stacks_inputs --logfile '$logfile' --summary summary.html ]]></command> <inputs> <param name="program" type="select" argument="--stacks-prog" label="Program which generated the stacks"> <option value="ustacks">ustacks (denovo)</option> <option value="pstacks">pstacks (refmap)</option> </param> <param name="logfile" argument="--logfile" format="txt" type="data" label="Log generated by the program" /> <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from ustacks or pstacks" /> </inputs> <outputs> <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="summary.html" /> </outputs> <tests> <test> <param name="program" value="ustacks"/> <param name="logfile" ftype="txt" value="ustacks/ustacks.out"/> <param name="input_col"> <collection type="list"> <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" /> <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" /> <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" /> <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" /> <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" /> <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> </collection> </param> <output name="output_summary"> <assert_contents> <has_text text="Stacks Statistics" /> </assert_contents> </output> </test> </tests> <help> <![CDATA[ .. class:: infomark **What it does** When given the output of ustacks or pstacks, this will generate a report containing various statistics about the detected stacks in a set of samples. -------- @STACKS_INFOS@ ]]> </help> <expand macro="citation" /> </tool>