Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
diff abundance_estimates_to_matrix.xml @ 1:fba77b1f69b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
| author | iuc |
|---|---|
| date | Fri, 18 Nov 2016 06:07:28 -0500 |
| parents | 77fc547df6ff |
| children | 8b5039bdf1f6 |
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--- a/abundance_estimates_to_matrix.xml Mon Aug 01 14:42:33 2016 -0400 +++ b/abundance_estimates_to_matrix.xml Fri Nov 18 06:07:28 2016 -0500 @@ -1,16 +1,17 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="3.14.0">bioconductor-edger</requirement> - <requirement type="package" version="0.6.0">salmon</requirement> + <requirement type="package" version="0.7.2">salmon</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ + #import re #for $entry in $samples: - ln -s "${entry.file}" "${entry.sample_name}" && + ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && #end for abundance_estimates_to_matrix.pl @@ -19,16 +20,11 @@ --cross_sample_norm ${additional_params.cross_sample_norm} #for $entry in $samples: - "${entry.sample_name}" + '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' #end for ]]></command> <inputs> - <repeat name="samples" title="Abundance estimates for samples"> - <param name="file" label="Add file" type="data" format="tabular"/> - <param name="sample_name" label="Sample name" type="text"> - <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> - </param> - </repeat> + <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> @@ -56,10 +52,7 @@ </outputs> <tests> <test> - <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -82,10 +75,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -108,10 +98,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> <param name="est_method" value="eXpress"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -134,10 +121,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="UpperQuartile"/> <output name="trans_counts"> @@ -159,10 +143,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts"> @@ -179,10 +160,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/salmon/quant.sf"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/salmon/quant.sf.genes"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> <param name="est_method" value="salmon"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts">