diff analyze_diff_expr.xml @ 7:d61afd68a493 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4

--- a/analyze_diff_expr.xml	Mon Jan 22 11:27:05 2018 -0500
+++ b/analyze_diff_expr.xml	Thu Jun 14 03:11:32 2018 -0400
@@ -1,12 +1,13 @@
-<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.2">
+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@">
     <description>from a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>
-        <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>
+        <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
+        <requirement type="package" version="1.30.0">bioconductor-goseq</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[
     ## DE results input files must be in the working directory and have suffix .DE_results
@@ -14,10 +15,10 @@
     #for $input in $DE_results
         #if re.search('.DE_results$',input.element_identifier)
             ## General case, where DE results files have been previously generated by run_de_analysis.pl
-            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
+            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
         #else
             ## Particular case, where DE results files have non-standard names
-            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
+            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
         #end if
         &&
     #end for
@@ -25,14 +26,14 @@
         ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
         #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
             ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
-            ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
+            ln -s '${DE_matrix}' "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
             &&
         #end for
     #end if
 
     analyze_diff_expr.pl
-        --matrix "${matrix}"
-        --samples "${samples}"
+        --matrix '${matrix}'
+        --samples '${samples}'
         -P ${p}
         -C ${c}
 
@@ -48,8 +49,8 @@
 
         #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
             --examine_GO_enrichment
-            --GO_annots "${$additional_params.GO_enrichment.GO_annots}"
-            --gene_lengths "${$additional_params.GO_enrichment.gene_lengths}"
+            --GO_annots '${$additional_params.GO_enrichment.GO_annots}'
+            --gene_lengths '${$additional_params.GO_enrichment.gene_lengths}'
         #end if
 
         --output results
@@ -162,8 +163,6 @@
             <param name="samples" value="count/samples.txt"/>
             <param name="DE_results">
                 <collection type="list">
-                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
-                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                     <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                 </collection>
             </param>
@@ -172,8 +171,6 @@
                     <param name="examine_GO_enrichment" value="yes"/>
                     <param name="DE_matrices">
                         <collection type="list">
-                            <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
-                            <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                             <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                         </collection>
                     </param>
@@ -187,7 +184,7 @@
                 <has_text text="--gene_lengths" />
             </assert_command>
             <output_collection name="GOseq_enrichment">
-                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched"/>
             </output_collection>
         </test>
     </tests>