diff data_manager/macros.xml @ 1:6127cd38980b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml	Mon Jun 24 11:36:07 2019 -0400
@@ -0,0 +1,68 @@
+<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. -->
+    <!-- STAR version to be used -->
+    <token name="@VERSION@">2.7.1a</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.
+    It can be found for any specific version of STAR with:
+    STAR -h | grep versionGenome
+    or by looking for the versionGenome parameter in source/parametersDefault
+    of STAR's source code -->
+    <token name="@IDX_VERSION@">2.7.1a</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">star</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="index_selection" token_with_gene_model="1">
+        <param argument="--genomeDir" name="genomeDir" type="select"
+        label="Select reference genome"
+        help="If your genome of interest is not listed, contact the Galaxy team">
+            <options from_data_table="rnastar_index2_versioned">
+                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
+                <filter type="static_value" column="5" value="@IDX_VERSION@" />
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No indexes are available for the selected input dataset" />
+            </options>
+        </param>
+    </xml>
+
+    <token name="@FASTQ_GZ_OPTION@">
+        --readFilesCommand zcat
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts635</citation>
+        </citations>
+    </xml>
+    <xml name="@SJDBOPTIONS@" token_optional="true">
+         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
+         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
+    </xml>
+    <xml name="dbKeyActions">
+        <actions>
+            <conditional name="refGenomeSource.geneSource">
+                <when value="indexed">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
+                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
+                        </option>
+                    </action>
+                </when>
+                <when value="history">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </xml>
+</macros>