Mercurial > repos > yhoogstrate > fuma

diff fuma.xml @ 9:b21145d59d9c draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/fuma commit 7bf6f3629e96bcaaed8770badd11366889efa99c
author erasmusmc
date Mon, 23 Jan 2017 09:41:08 -0500
parents 8366a8c82a7a
children
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--- a/fuma.xml	Mon Feb 08 04:56:40 2016 -0500
+++ b/fuma.xml	Mon Jan 23 09:41:08 2017 -0500
@@ -1,14 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="fuma" name="FuMa" version="2.11.3-g0">
+<tool id="fuma" name="FuMa" version="3.0.5-g0">
     <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description>
-    
+
     <requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="2.11.3">fuma</requirement>
+        <requirement type="package" version="3.0.5">fuma</requirement>
     </requirements>
-    
+
     <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->
-    
+
     <command><![CDATA[
         #import pipes
         
@@ -25,9 +24,9 @@
             #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
         #end for
         
-        #set $gene_annotations_str = " ".join(gene_annotations)
-        #set $samples_str = " ".join(samples)
-        #set $links_str = " ".join(links)
+        #set $gene_annotations_str = "'"+"' '".join(gene_annotations)+"'"
+        #set $samples_str = "'"+"' '".join(samples)+"'"
+        #set $links_str = "'"+"' '".join(links)+"'"
         
         fuma 
           -m
@@ -49,12 +48,12 @@
         #else
           -f $params.output_format.value
         #end if
-          -o $fuma_overview ; 
+          -o '${fuma_overview}'
         
         
         #if $params.output_format.value == "list_boolean"
-            fuma-list-to-boolean-list -o tmp.txt $fuma_overview ;
-            mv tmp.txt $fuma_overview
+            && fuma-list-to-boolean-list -o tmp.txt '${fuma_overview}'
+            && mv tmp.txt '${fuma_overview}'
         #end if
     ]]></command>
     
@@ -94,7 +93,9 @@
                 <param name="long_gene_size" type="hidden" value="200000" />
             </when>
             <when value="full">
-                <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative">
+                <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets"
+                       help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative"
+                       argument="-m">
                     <option value="overlap">Overlap</option>
                     <option value="subset" selected="True">Subset</option>
                     <option value="egm">Exact Geneset Matching (EGM)</option>
@@ -111,7 +112,9 @@
                     label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)"
                     help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />
                 
-                <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size" help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a 'long gene' as reported the output. Use 0 to disable this feature (--long-gene-size)" />
+                <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size"
+                       help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a 'long gene' as reported the output. Use 0 to disable this feature"
+                       argument="--long-gene-size" />
                 
                 <param name="output_format" type="select" label="Output format">
                     <option value="list_boolean" selected="true">List (Boolean)</option>
@@ -127,27 +130,70 @@
     </outputs>
     
     <tests>
+        <!-- Large tests, take long
         <test>
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
-                <param name="datasets_0|format" value="chimerascan" />
-                <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
-                <param name="datasets_1|format" value="defuse" />
-                <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
-                <param name="datasets_2|format" value="fusionmap" />
-                <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
-                <param name="datasets_3|format" value="fusionmap" />
-                <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
+            <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
+            <param name="datasets_0|format" value="chimerascan" />
+            <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
+            <param name="datasets_1|format" value="defuse" />
+            <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
+            <param name="datasets_2|format" value="fusionmap" />
+            <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
+            <param name="datasets_3|format" value="fusionmap" />
+            <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+            
+            <param name="settingsType" value="full" />
+            
+            <param name="matching_method" value="subset" />
+            <param name="strand_specific_matching" value=" - - strand-specific-matching" />
+            <param name="acceptor_donor_order_specific_matchig" value=" - -acceptor-donor-order-specific-matching" />
+            <param name="long_gene_size" value="200000" />
+            <param name="output_format" value="list_boolean" />
+            
+            <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />
+        </test>
+        <test>
+            <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" />
+            <param name="datasets_0|format" value="fusionmap" />
+            <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" />
+            <param name="datasets_1|format" value="fusionmap" />
+            <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
+            <param name="datasets_0|format" value="chimerascan" />
+            <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+            
+            <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
+            <param name="datasets_1|format" value="defuse" />
+            <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+            
+            <param name="settingsType" value="full" />
+            
+            <param name="matching_method" value="subset" />
+            <param name="strand_specific_matching" value="False" />
+            <param name="acceptor_donor_order_specific_matchig" value="False" />
+            <param name="long_gene_size" value="200000" />
+            <param name="output_format" value="list_boolean" />
+            
+            <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />
+        </test>
+        -->
+        <test>
+            <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" />
+            <param name="datasets_0|format" value="fusionmap" />
+            <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" />
+            <param name="datasets_1|format" value="fusionmap" />
+            <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
             
             <param name="settingsType" value="full" />
             
@@ -157,29 +203,16 @@
             <param name="long_gene_size" value="200000" />
             <param name="output_format" value="list_boolean" />
             
-            <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />
+            <output name="fuma_overview" file="edgren_test_03_specific_matching_output.txt" />
         </test>
         <test>
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
-                <param name="datasets_0|format" value="chimerascan" />
-                <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
-                <param name="datasets_1|format" value="defuse" />
-                <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
-                <param name="datasets_2|format" value="fusionmap" />
-                <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
-            <!-- <repeat name="datasets"> -->
-                <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
-                <param name="datasets_3|format" value="fusionmap" />
-                <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
-            <!-- </repeat> -->
+            <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" />
+            <param name="datasets_0|format" value="fusionmap" />
+            <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
+
+            <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" />
+            <param name="datasets_1|format" value="fusionmap" />
+            <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
             
             <param name="settingsType" value="full" />
             
@@ -189,7 +222,7 @@
             <param name="long_gene_size" value="200000" />
             <param name="output_format" value="list_boolean" />
             
-            <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />
+            <output name="fuma_overview" file="edgren_test_04_unspecific_matching_output.txt" />
         </test>
     </tests>