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comparison telescope_assign.xml @ 1:54144e379f6d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
author iuc
date Wed, 24 Aug 2022 22:30:02 +0000
parents 71fcee7f54df
children
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0:71fcee7f54df 1:54144e379f6d
1 <?xml version="1.0"?> 1 <tool id="telescope_assign" name="Reassign reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <tool id="telescope_assign" name="Reassign reads" version="@VERSION@">
3 <description>with TELESCOPE using a statistical model</description> 2 <description>with TELESCOPE using a statistical model</description>
3 <xrefs>
4 <xref type="bio.tools">Telescope-expression</xref>
5 </xrefs>
4 <macros> 6 <macros>
5 <token name="@VERSION@">1.0.3</token> 7 <token name="@TOOL_VERSION@">1.0.3</token>
8 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 9 </macros>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@VERSION@">telescope</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">telescope</requirement>
9 <requirement type="package" version="1.9">samtools</requirement> 12 <requirement type="package" version="1.9">samtools</requirement>
10 </requirements> 13 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
12 mkdir tempdir && 15 mkdir tempdir &&
13 mkdir outdir && 16 mkdir outdir &&
17
14 telescope assign '$input_alignment' '$input_gtf' 18 telescope assign '$input_alignment' '$input_gtf'
15 --tempdir tempdir 19 --tempdir tempdir
16 --outdir outdir 20 --outdir outdir
17 --ncpu \${GALAXY_SLOTS:-1} 21 ## Not supported https://github.com/mlbendall/telescope/blob/6cd55256c6016feffdbfe10346bfecfcb1e30965/README.md?plain=1#L129
22 ## --ncpu \${GALAXY_SLOTS:-1}
18 $updated_sam 23 $updated_sam
19 #if str($advanced.advanced_options) == 'select': 24 #if str($advanced.advanced_options) == 'select':
20 --reassign_mode $advanced.reassign_mode 25 --reassign_mode $advanced.reassign_mode
21 --conf_prob $advanced.conf_prob 26 --conf_prob $advanced.conf_prob
22 --overlap_mode $advanced.overlap_mode 27 --overlap_mode $advanced.overlap_mode
29 $advanced.use_likelihood 34 $advanced.use_likelihood
30 #end if 35 #end if
31 #if $updated_sam 36 #if $updated_sam
32 && 37 &&
33 if [ -f outdir/telescope-updated.bam ] ; then 38 if [ -f outdir/telescope-updated.bam ] ; then
34 samtools sort outdir/telescope-updated.bam > '$updated_alignment' ; 39 samtools sort -T "\${TMPDIR:-.}" outdir/telescope-updated.bam > '$updated_alignment' ;
35 else 40 else
36 echo 'Updated alignment file not found.' ; 41 echo 'Updated alignment file not found.' ;
37 exit 1 ; 42 exit 1 ;
38 fi 43 fi
39 #end if 44 #end if