Mercurial > repos > yhoogstrate > star_fusion

changeset 2:810f5b815c18 draft

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planemo upload for repository http://bioinf-galaxian/galaxy/ commit 3c38f42a143a056b0de35f03a0067d87a1d940c2-dirty
author yhoogstrate
date Wed, 24 Aug 2016 07:17:11 -0400
parents 967800209940
children f36e648ed12a
files star_fusion.xml
diffstat 1 files changed, 23 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/star_fusion.xml	Wed Aug 24 04:55:00 2016 -0400
+++ b/star_fusion.xml	Wed Aug 24 07:17:11 2016 -0400
@@ -35,7 +35,7 @@
         
         ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
         prep_genome_lib.pl
-            --genome_fa '${ownFile}'
+            --genome_fa '${fasta_type.ownFile}'
             --gtf '${geneModel}'
             --blast_pairs "${blast_pairs}\$gzip_suffix"
             --CPU \${GALAXY_SLOTS:-1}
@@ -98,11 +98,26 @@
         </conditional>
 
         <!-- Genome source. -->
-        <param name="ownFile"
-               type="data"
-               format="fasta"
-               metadata_name="dbkey"
-               label="Select the reference genome (FASTA file)"/>
+        <conditional name="fasta_type">
+            <param name="fasta_type_selector" type="select" label="Source for sequence to search">
+                <option value="cached">Locally Cached sequences</option>
+                <option value="history" selected="true">Sequences from your history</option>
+            </param>
+            <when value="cached">
+                <param name="ownFile"
+                       type="select" label="Genome to search">
+                    <options from_data_table="all_fasta" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="ownFile"
+                       type="data"
+                       format="fasta"
+                       metadata_name="dbkey"
+                       label="Select the reference genome (FASTA file)"/>
+            </when>
+        </conditional>
+        
         <param name="geneModel"
                type="data"
                format="gff3,gtf"
@@ -166,7 +181,7 @@
         <test>
             <param name="input_source" value="use_chimeric" />
             <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
-            <param name="genomeSource" value="history" />
+            <param name="fasta_type_selector" value="history" />
             <param name="ownFile" ftype="fasta" value="test1.fa" />
             <param name="geneModel" ftype="gtf" value="test1.gtf" />
             <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
@@ -183,7 +198,7 @@
         <test>
             <param name="input_source" value="use_fastq" />
             <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
-            <param name="genomeSource" value="history" />
+            <param name="fasta_type_selector" value="history" />
             <param name="ownFile" ftype="fasta" value="test1.fa" />
             <param name="geneModel" ftype="gtf" value="test1.gtf" />
             <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />