diff data_manager/macros.xml @ 4:039890bdcb62 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 93138516106c74b1ccc70d2d946e6eaa29c7c1a3-dirty

--- a/data_manager/macros.xml	Mon Jun 24 12:27:02 2019 -0400
+++ b/data_manager/macros.xml	Wed Oct 16 03:33:53 2019 -0400
@@ -1,10 +1,11 @@
 <macros>
     <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
     whenever you make changes to the following two version tokens!
-    The data manager uses a symlink to this macro file to keep the versions in
-    sync. -->
+    The data manager uses a symlink to this macro file to keep the STAR and
+    the index versions in sync, but you should manually adjust the +galaxy
+    version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.1a</token>
+    <token name="@VERSION@">2.7.2b</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -21,7 +22,7 @@
         </requirements>
     </xml>
 
-    <xml name="index_selection" token_with_gene_model="1">
+    <xml name="index_selection" token_with_gene_model="0">
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
@@ -65,4 +66,100 @@
             </conditional>
         </actions>
     </xml>
+    <token name="@TEMPINDEX@"><![CDATA[
+    ## Create temporary index for custom reference
+    #if str($refGenomeSource.geneSource) == 'history':
+        mkdir -p tempstargenomedir &&
+        STAR
+            --runMode genomeGenerate
+            --genomeDir 'tempstargenomedir'
+            --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
+            ## Handle difference between indices with/without annotations
+            #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+                --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
+                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+                    --sjdbGTFtagExonParentTranscript Parent
+                #end if
+            #end if
+            #if str($refGenomeSource.genomeSAindexNbases):
+                --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
+            #end if
+            --runThreadN \${GALAXY_SLOTS:-4}
+        &&
+    #end if
+    ]]></token>
+    <token name="@REFGENOMEHANDLING@" ><![CDATA[
+    --runThreadN \${GALAXY_SLOTS:-4}
+    --genomeLoad NoSharedMemory
+    --genomeDir
+    #if str($refGenomeSource.geneSource) == 'history':
+        tempstargenomedir
+    #else:
+        '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
+        ## Handle difference between indices with/without annotations
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
+            #if $refGenomeSource.GTFconditional.sjdbGTFfile:
+                --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
+                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+                    --sjdbGTFtagExonParentTranscript Parent
+                #end if
+            #end if
+        #end if
+        #end if
+        ]]></token>
+    <xml name="stdio" >
+        <stdio>
+            <regex match="FATAL error" source="both" level="fatal"/>
+            <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
+            <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
+            <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
+            <yield />
+        </stdio>
+    </xml>
+    <xml name="refgenomehandling" >
+        <conditional name="refGenomeSource">
+            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
+                <option value="indexed" selected="true">Use a built-in index</option>
+                <option value="history">Use reference genome from history and create temporary index</option>
+            </param>
+            <when value="indexed">
+                <conditional name="GTFconditional">
+                    <param name="GTFselect" type="select"
+                           label="Reference genome with or without an annotation"
+                           help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
+                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
+                        <option value="with-gtf">use genome reference with builtin gene-model</option>
+                    </param>
+                    <when value="with-gtf">
+                        <expand macro="index_selection" with_gene_model="1" />
+                    </when>
+                    <when value="without-gtf">
+                        <expand macro="index_selection" with_gene_model="0" />
+                        <expand macro="@SJDBOPTIONS@" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="history">
+                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
+                <!-- Currently, this parameter is not exposed in the wrapper,
+                     but used only in the tests to avoid excessive index sizes for
+                     the tiny test genomes. -->
+                <param name="genomeSAindexNbases" type="hidden" value="" />
+                <conditional name="GTFconditional">
+                    <param name="GTFselect" type="select"
+                           label="Build index with our without known splice junctions annotation"
+                           help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
+                        <option value="without-gtf">build index without gene-model</option>
+                        <option value="with-gtf">build index with gene-model</option>
+                    </param>
+                    <when value="with-gtf">
+                        <expand macro="@SJDBOPTIONS@" optional="false"/>
+                    </when>
+                    <when value="without-gtf" />
+                </conditional>
+            </when>
+        </conditional>
+    </xml>
 </macros>