Mercurial > repos > iuc > trinity_samples_qccheck

diff samples_qccheck.xml @ 9:c5cce95aa90a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:10:27 -0400
parents 6ac9b8130aa2
children 001318fc2916
line wrap: on
line diff
--- a/samples_qccheck.xml	Mon Jan 22 11:25:29 2018 -0500
+++ b/samples_qccheck.xml	Thu Jun 14 03:10:27 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>