Previous changeset 7:1b7800489efb (2016-06-20) Next changeset 9:8bd817614cc8 (2016-07-12) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a |
modified:
abundance_estimates_to_matrix.xml run_DE_analysis.xml samples_qccheck.xml |
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diff -r 1b7800489efb -r 258c64019e50 abundance_estimates_to_matrix.xml --- a/abundance_estimates_to_matrix.xml Mon Jun 20 11:44:50 2016 -0400 +++ b/abundance_estimates_to_matrix.xml Tue Jun 28 12:22:40 2016 -0400 |
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@@ -1,4 +1,4 @@ -<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1"> +<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1.1"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <requirements> <requirement type="package" version="2.1.1">trinity</requirement> @@ -9,7 +9,7 @@ </stdio> <command><![CDATA[ #for $entry in $samples: - ln -s "${entry.file}" "${entry.sample_name}.tsv" && + ln -s "${entry.file}" "${entry.sample_name}" && #end for abundance_estimates_to_matrix.pl @@ -18,7 +18,7 @@ --cross_sample_norm ${additional_params.cross_sample_norm} #for $entry in $samples: - "${entry.sample_name}.tsv" + "${entry.sample_name}" #end for ]]></command> <inputs> |
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diff -r 1b7800489efb -r 258c64019e50 run_DE_analysis.xml --- a/run_DE_analysis.xml Mon Jun 20 11:44:50 2016 -0400 +++ b/run_DE_analysis.xml Tue Jun 28 12:22:40 2016 -0400 |
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@@ -79,10 +79,10 @@ </inputs> <outputs> <collection name="DE_results" type="list" label="Differential expression results on ${on_string}"> - <discover_datasets pattern="(?P<name>.+)\.DE_results" ext="tabular" directory="results" visible="true" /> + <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> </collection> <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> - <discover_datasets pattern="(?P<name>.+)\.pdf" ext="pdf" directory="results" visible="true" /> + <discover_datasets pattern="(?P<name>.+)\.pdf$" ext="pdf" directory="results" /> </collection> </outputs> <tests> |
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diff -r 1b7800489efb -r 258c64019e50 samples_qccheck.xml --- a/samples_qccheck.xml Mon Jun 20 11:44:50 2016 -0400 +++ b/samples_qccheck.xml Tue Jun 28 12:22:40 2016 -0400 |
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@@ -9,41 +9,41 @@ <exit_code range="1:"/> </stdio> <command><![CDATA[ - + ln -s "${matrix}" "input.matrix" - + && - + PtR --matrix "input.matrix" - + --samples "${samples}" - + --CPM --log2 --compare_replicates - + && - + PtR --matrix "input.matrix" - + --samples "${samples}" - + --CPM --log2 --sample_cor_matrix - + && - + PtR --matrix "input.matrix" - + --samples "${samples}" - + --CPM --log2 --prin_comp 3 - + && mkdir out_pdf && mv *rep_compare.pdf out_pdf/ && mv *sample_cor_matrix.pdf out_pdf/ && mv *principal_components.pdf out_pdf/ - + ]]></command> <inputs> <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> @@ -51,7 +51,7 @@ </inputs> <outputs> <collection name="reports" type="list" label="Quality check result files on ${on_string}"> - <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" /> + <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" /> </collection> </outputs> <tests> @@ -106,7 +106,7 @@ .. _Trinity: http://trinityrnaseq.github.io ]]> </help> - + <citations> <citation type="doi">10.1038/nbt.1883</citation> </citations> |