Mercurial > repos > iuc > trinity_samples_qccheck
diff samples_qccheck.xml @ 9:226663afe49c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 03:13:56 -0400 |
| parents | 8bec0d476fa0 |
| children | b58468eb4e64 |
line wrap: on
line diff
--- a/samples_qccheck.xml Mon Jan 22 11:29:45 2018 -0500 +++ b/samples_qccheck.xml Thu Jun 14 03:13:56 2018 -0400 @@ -1,23 +1,24 @@ -<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@"> <description>for transcript quantification</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> - <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> + <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> + <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement> <requirement type="package" version="2.0.6">r-cluster</requirement> + <requirement type="package" version="1.1.24">r-fastcluster</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ - ln -f -s "${matrix}" "input.matrix" + ln -f -s '${matrix}' "input.matrix" && PtR --matrix "input.matrix" - --samples "${samples}" + --samples '${samples}' --CPM --log2 --compare_replicates @@ -26,7 +27,7 @@ PtR --matrix "input.matrix" - --samples "${samples}" + --samples '${samples}' --CPM --log2 --sample_cor_matrix @@ -35,7 +36,7 @@ PtR --matrix "input.matrix" - --samples "${samples}" + --samples '${samples}' --CPM --log2 --prin_comp 3 @@ -62,7 +63,7 @@ <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> - <element name="input.matrix.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.principal_components.pdf"/> + <element name="input.matrix.CPM.log2.prcomp.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf"/> <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf"/> </output_collection> </test>