Mercurial > repos > iuc > telescope_assign
comparison telescope_assign.xml @ 1:2d8c943f3e8d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
author | iuc |
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date | Wed, 24 Aug 2022 22:30:35 +0000 |
parents | 66ff74923224 |
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0:66ff74923224 | 1:2d8c943f3e8d |
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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 |