Mercurial > repos > iuc > stacks_stats
diff 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 |
parents | |
children | 93b16407d6e9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_stats.xml Thu Apr 27 04:18:05 2017 -0400 @@ -0,0 +1,82 @@ +<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>