Mercurial > repos > devteam > bam_to_sam

annotate macros.xml @ 9:3c661e57a88f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:24:55 +0000
parents a53efedba9e7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
1 <macros>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
2 <xml name="requirements">
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
3 <requirements>
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
3
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
5 <yield/>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
6 </requirements>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
7 </xml>
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
8 <!-- NOTE: for some tools only the version of the requirement but not the
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
9 tool's version is controlled by the TOOL_VERSION token
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
10 (because their version is ahead of the requirement version ..
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
11 please only bump the minor version in order to let the requirement
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
12 version catch up eventually). To find the tools check:
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
13 `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
9
3c661e57a88f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 8
diff changeset
14 <token name="@TOOL_VERSION@">1.20</token>
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
15 <token name="@VERSION_SUFFIX@">2</token>
9
3c661e57a88f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 8
diff changeset
16 <token name="@PROFILE@">22.05</token>
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
17 <token name="@FLAGS@"><![CDATA[
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
18 #set $flags = 0
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
19 #if $filter
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
20 #set $flags = sum(map(int, str($filter).split(',')))
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
21 #end if
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
22 ]]></token>
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
23 <token name="@PREPARE_IDX@"><![CDATA[
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
24 ##prepare input and indices
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
25 ln -s '$input' infile &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
26 #if $input.is_of_type('bam'):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
27 #if str( $input.metadata.bam_index ) != "None":
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
28 ln -s '${input.metadata.bam_index}' infile.bai &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
29 #else:
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
30 samtools index infile infile.bai &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
31 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
32 #elif $input.is_of_type('cram'):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
33 #if str( $input.metadata.cram_index ) != "None":
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
34 ln -s '${input.metadata.cram_index}' infile.crai &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
35 #else:
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
36 samtools index infile infile.crai &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
37 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
38 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
39 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
40 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
41 ##prepare input and indices
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
42 #for $i, $bam in enumerate( $input_bams ):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
43 ln -s '$bam' '${i}' &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
44 #if $bam.is_of_type('bam'):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
45 #if str( $bam.metadata.bam_index ) != "None":
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
46 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
47 #else:
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
48 samtools index '${i}' '${i}.bai' &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
49 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
50 #elif $bam.is_of_type('cram'):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
51 #if str( $bam.metadata.cram_index ) != "None":
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
52 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
53 #else:
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
54 samtools index '${i}' '${i}.crai' &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
55 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
56 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
57 #end for
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
58 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
59 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
60 ## Make the user-selected reference genome, if any, accessible through
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
61 ## a shell variable $reffa, index the reference if necessary, and make
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
62 ## the fai-index file available through a shell variable $reffai.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
63
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
64 ## For a cached genome simply sets the shell variables to point to the
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
65 ## genome file and its precalculated index.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
66 ## For a genome from the user's history, if that genome is a plain
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
67 ## fasta file, the code creates a symlink in the pwd, creates the fai
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
68 ## index file next to it, then sets the shell variables to point to the
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
69 ## symlink and its index.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
70 ## For a fasta.gz dataset from the user's history, it tries the same,
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
71 ## but this will only succeed if the file got compressed with bgzip.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
72 ## For a regular gzipped file samtools faidx will fail, in which case
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
73 ## the code falls back to decompressing to plain fasta before
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
74 ## reattempting the indexing.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
75 ## Indexing of a bgzipped file produces a regular fai index file *and*
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
76 ## a compressed gzi file. The former is identical to the fai index of
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
77 ## the uncompressed fasta.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
78
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
79 ## If the user has not selected a reference (it's an optional parameter
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
80 ## in some samtools wrappers), a cheetah boolean use_ref is set to
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
81 ## False to encode that fact.
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
82
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
83 #set use_ref=True
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
84 #if $addref_cond.addref_select == "history":
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
85 #if $addref_cond.ref.is_of_type('fasta'):
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
86 reffa="reference.fa" &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
87 ln -s '${addref_cond.ref}' \$reffa &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
88 samtools faidx \$reffa &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
89 #else:
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
90 reffa="reference.fa.gz" &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
91 ln -s '${addref_cond.ref}' \$reffa &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
92 {
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
93 samtools faidx \$reffa ||
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
94 {
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
95 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
96 gzip -dc \$reffa > reference.fa &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
97 reffa="reference.fa" &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
98 samtools faidx \$reffa;
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
99 }
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
100 } &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
101 #end if
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
102 reffai=\$reffa.fai &&
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
103 #elif $addref_cond.addref_select == "cached":
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
104 ## in case of cached the absolute path is used which allows to read
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
105 ## a cram file without specifying the reference
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
106 reffa='${addref_cond.ref.fields.path}' &&
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
107 reffai=\$reffa.fai &&
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
108 #else
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
109 #set use_ref=False
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
110 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
111 ]]></token>
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
112
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
113 <xml name="optional_reference" token_help="" token_argument="">
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
114 <conditional name="addref_cond">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
115 <param name="addref_select" type="select" label="Use a reference sequence">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
116 <help>@HELP@</help>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
117 <option value="no">No</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
118 <option value="history">Use a genome/index from the history</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
119 <option value="cached">Use a built-in genome</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
120 </param>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
121 <when value="no"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
122 <when value="history">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
123 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
124 </when>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
125 <when value="cached">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
126 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
127 <options from_data_table="fasta_indexes">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
128 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
129 </options>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
130 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
131 </param>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
132 </when>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
133 </conditional>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
134 </xml>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
135 <xml name="mandatory_reference" token_help="" token_argument="">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
136 <conditional name="addref_cond">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
137 <param name="addref_select" type="select" label="Use a reference sequence">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
138 <help>@HELP@</help>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
139 <option value="history">Use a genome/index from the history</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
140 <option value="cached">Use a built-in genome</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
141 </param>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
142 <when value="history">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
143 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
144 </when>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
145 <when value="cached">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
146 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
147 <options from_data_table="fasta_indexes">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
148 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
149 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
150 </options>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
151 </param>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
152 </when>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
153 </conditional>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
154 </xml>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
155
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
156
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
157 <token name="@ADDTHREADS@"><![CDATA[
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
158 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
159 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
160 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
161 <token name="@ADDMEMORY@"><![CDATA[
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
162 ##compute the number of memory available to samtools sort (-m)
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
163 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
164 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
165 ((addmemory=addmemory*75/100)) &&
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
166 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
167 <xml name="seed_input">
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
168 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
169 </xml>
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
170 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
171 <option value="1" selected="@S1@">Read is paired</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
172 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
173 <option value="4" selected="@S4@">Read is unmapped</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
174 <option value="8" selected="@S8@">Mate is unmapped</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
175 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
176 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
177 <option value="64" selected="@S64@">Read is the first in a pair</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
178 <option value="128" selected="@S128@">Read is the second in a pair</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
179 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
180 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
181 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
182 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
183 </xml>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
184
7
10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 6
diff changeset
185 <!-- region specification macros and tokens for tools that allow the specification
6
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
186 of region by bed file / space separated list of regions -->
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
187 <token name="@REGIONS_FILE@"><![CDATA[
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
188 #if $cond_region.select_region == 'tab':
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
189 -t '$cond_region.targetregions'
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
190 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
191 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
192 <token name="@REGIONS_MANUAL@"><![CDATA[
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
193 #if $cond_region.select_region == 'text':
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
194 #for $i, $x in enumerate($cond_region.regions_repeat):
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
195 '${x.region}'
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
196 #end for
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
197 #end if
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
198 ]]></token>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
199 <xml name="regions_macro">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
200 <conditional name="cond_region">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
201 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
202 <option value="no" selected="True">No</option>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
203 <option value="text">Manualy specify regions</option>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
204 <option value="tab">Regions from tabular file</option>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
205 </param>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
206 <when value="no"/>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
207 <when value="text">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
208 <repeat name="regions_repeat" min="1" default="1" title="Regions">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
209 <param name="region" type="text" label="region" help="format chr:from-to">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
210 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
211 </param>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
212 </repeat>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
213 </when>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
214 <when value="tab">
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
215 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
216 </when>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
217 </conditional>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
218 </xml>
88eedb4abea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 5
diff changeset
219
3
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
220 <xml name="citations">
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
221 <citations>
8
a53efedba9e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 7
diff changeset
222 <citation type="doi">10.1093/gigascience/giab008</citation>
3
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
223 </citations>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
224 </xml>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
225 <xml name="version_command">
5
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 4
diff changeset
226 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
3
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
227 </xml>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
228 <xml name="stdio">
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
229 <stdio>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
230 <exit_code range="1:" level="fatal" description="Error" />
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
231 </stdio>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
232 </xml>
c1419fa820c6 Uploaded
devteam
parents:
diff changeset
233 </macros>