Mercurial > repos > ieguinoa > data_manager_star_index_custom

comparison data_manager/rna_star_index_builder.xml @ 1:67c59c6576db draft

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author ieguinoa
date Thu, 26 Aug 2021 20:04:16 +0000
parents e23440b3332a
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0:e23440b3332a 1:67c59c6576db
9 <requirement type="package" version="3.7">python</requirement> 9 <requirement type="package" version="3.7">python</requirement>
10 </expand> 10 </expand>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 if [ -z "\$GALAXY_MEMORY_MB" ] ; then 13 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
14 GALAXY_MEMORY_BYTES=31000000000 ; 14 GALAXY_MEMORY_BYTES=310000000000 ;
15 else 15 else
16 GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ; 16 GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ;
17 fi ; 17 fi ;
18 18
19 #import os 19 #import os
26 --runMode genomeGenerate 26 --runMode genomeGenerate
27 --genomeFastaFiles '${all_fasta_source.fields.path}' 27 --genomeFastaFiles '${all_fasta_source.fields.path}'
28 --genomeDir '${target_directory}' 28 --genomeDir '${target_directory}'
29 --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES} 29 --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES}
30 #if $GTFconditional.GTFselect == "withGTF": 30 #if $GTFconditional.GTFselect == "withGTF":
31 #if $GTFconditional.GTF_source_conditional == "builtin_gff": 31 #if $GTFconditional.GTF_source_conditional.GTF_source_select == "builtin_gff":
32 --sjdbGTFfile '${GTFconditional.GTF_source_conditional.all_gff_source.path}' 32 --sjdbGTFfile '${GTFconditional.GTF_source_conditional.all_gff_source.fields.path}'
33 #else 33 #else
34 --sjdbGTFfile '${GTFconditional.GTF_source_conditional.sjdbGTFfile}' 34 --sjdbGTFfile '${GTFconditional.GTF_source_conditional.sjdbGTFfile}'
35 #end if 35 #end if
36 --sjdbOverhang ${GTFconditional.sjdbOverhang} 36 --sjdbOverhang ${GTFconditional.sjdbOverhang}
37 #end if 37 #end if
74 <param name="GTF_source_select" type="select" label="Select source of annotation GTF/GFF" > 74 <param name="GTF_source_select" type="select" label="Select source of annotation GTF/GFF" >
75 <option value="builtin_gff">Use a builtin GTF/GFF</option> 75 <option value="builtin_gff">Use a builtin GTF/GFF</option>
76 <option value="external_gff">Use an external GTF/GFF</option> 76 <option value="external_gff">Use an external GTF/GFF</option>
77 </param> 77 </param>
78 <when value="builtin_gff"> 78 <when value="builtin_gff">
79 <param name="all_gff_source" type="select" label="Source FASTA Sequence"> 79 <param name="all_gff_source" type="select" label="Select source GFF/GTF File">
80 <options from_data_table="all_gff"/> 80 <options from_data_table="all_gff"/>
81 </param> 81 </param>
82 </when> 82 </when>
83 <when value="external_gff"> 83 <when value="external_gff">
84 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> 84 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>