Mercurial > repos > iuc > ruvseq

diff ruvseq.xml @ 1:c24765926774 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
author iuc
date Tue, 26 Mar 2019 06:25:38 -0400
parents 61dffb20b6f9
children fed9d0350d72
line wrap: on
line diff
--- a/ruvseq.xml	Wed Sep 05 15:54:16 2018 -0400
+++ b/ruvseq.xml	Tue Mar 26 06:25:38 2019 -0400
@@ -1,11 +1,12 @@
-<tool id="ruvseq" name="Remove Unwanted Variation" version="1.12.0">
+<tool id="ruvseq" name="Remove Unwanted Variation" version="1.16.0">
     <description>from RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="1.12.0">bioconductor-ruvseq</requirement>
-        <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
-        <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="0.6.5">r-ggrepel</requirement>
+        <requirement type="package" version="1.16.0">bioconductor-ruvseq</requirement>
+        <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
+        <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
+        <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="0.8.0">r-ggrepel</requirement>
+        <requirement type="package" version="1.20.2">r-getopt</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -44,6 +45,7 @@
 
 --min_k $min_k
 --max_k $max_k
+--min_mean_count $min_mean_count
 
 #if $tximport.tximport_selector == 'tximport':
     --txtype $tximport.txtype
@@ -136,19 +138,19 @@
                 <element name="batch_effects_control_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
                 <element name="batch_effects_replicate_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
                 <element name="batch_effects_residual_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -170,19 +172,19 @@
                 <element name="batch_effects_control_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
                 <element name="batch_effects_replicate_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
                 <element name="batch_effects_residual_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/>
+                        <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -202,24 +204,25 @@
             <param name="txtype" value="sailfish"/>
             <param name="mapping_format_selector" value="tabular"/>
             <param name="tabular_file" value="tx2gene.tab"/>
+            <param name="min_mean_count" value="0"/>
             <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/>
             <output_collection name="unwanted_variation" type="list">
                 <element name="batch_effects_control_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.28.*"/>
+                        <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> 
                     </assert_contents>
                 </element>
                 <element name="batch_effects_replicate_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.44.*"/>
+                        <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> 
                     </assert_contents>
                 </element>
                 <element name="batch_effects_residual_method_k1">
                     <assert_contents>
                         <has_text_matching expression="identifier\tcondition\tW_1"/>
-                        <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.22.*"/>
+                        <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> 
                     </assert_contents>
                 </element>
             </output_collection>