Mercurial > repos > devteam > samtools_sort

annotate macros.xml @ 9:17bed26ad17e draft

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/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
author iuc
date Wed, 19 Sep 2018 09:53:20 -0400
parents 71d5c34fef4e
children c15c63771494
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
1 <macros>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
2 <xml name="requirements">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
3 <requirements>
9
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
6
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
5 <yield/>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
6 </requirements>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
7 </xml>
9
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
8 <token name="@TOOL_VERSION@">1.9</token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
10 <token name="@PREPARE_IDX@"><![CDATA[
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
11 ##prepare input and indices
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
12 ln -s '$input' infile &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
13 #if $input.is_of_type('bam'):
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
14 #if str( $input.metadata.bam_index ) != "None":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
15 ln -s '${input.metadata.bam_index}' infile.bai &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
16 #else:
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
17 samtools index infile infile.bai &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
18 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
19 #elif $input.is_of_type('cram'):
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
20 #if str( $input.metadata.cram_index ) != "None":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
21 ln -s '${input.metadata.cram_index}' infile.crai &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
22 #else:
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
23 samtools index infile infile.crai &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
24 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
25 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
26 ]]></token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
28 ##prepare input and indices
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
29 #for $i, $bam in enumerate( $input_bams ):
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
30 ln -s '$bam' '${i}' &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
31 #if $bam.is_of_type('bam'):
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
32 #if str( $bam.metadata.bam_index ) != "None":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
33 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
34 #else:
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
35 samtools index '${i}' '${i}.bai' &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
36 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
37 #elif $bam.is_of_type('cram'):
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
38 #if str( $bam.metadata.cram_index ) != "None":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
39 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
40 #else:
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
41 samtools index '${i}' '${i}.crai' &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
42 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
43 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
44 #end for
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
45 ]]></token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
48 ##and sets the -t/-T parameters accordingly:
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
49 ##- in case of history a symbolic link is used because samtools (view) will generate
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
50 ## the index which might not be possible in the directory containing the fasta file
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
51 ##- in case of cached the absolute path is used which allows to read the cram file
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
52 ## without specifying the reference
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
53 #if $addref_cond.addref_select == "history":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
54 ln -s '${addref_cond.ref}' reference.fa &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
55 samtools faidx reference.fa &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
56 #set reffa=str($addref_cond.ref)
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
57 #set reffai="reference.fa.fai"
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
58 #elif $addref_cond.addref_select == "cached":
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
59 #set reffa=str($addref_cond.ref.fields.path)
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
60 #set reffai=str($addref_cond.ref.fields.path)
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
61 #else
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
62 #set reffa=None
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
63 #set reffai=None
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
64 #end if
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
65 ]]></token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
66 <token name="@ADDTHREADS@"><![CDATA[
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
69 ]]></token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
70
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
71 <token name="@ADDMEMORY@"><![CDATA[
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
72 ##compute the number of memory available to samtools sort (-m)
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
73 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
74 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
75 ((addmemory=addmemory*75/100)) &&
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
76 ]]></token>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
77 <xml name="flag_options">
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
78 <option value="1">read is paired</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
79 <option value="2">read is mapped in a proper pair</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
80 <option value="4">read is unmapped</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
81 <option value="8">mate is unmapped</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
82 <option value="16">read reverse strand</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
83 <option value="32">mate reverse strand</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
84 <option value="64">read is the first in a pair</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
85 <option value="128">read is the second in a pair</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
86 <option value="256">alignment or read is not primary</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
87 <option value="512">read fails platform/vendor quality checks</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
88 <option value="1024">read is a PCR or optical duplicate</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
89 <option value="2048">supplementary alignment</option>
17bed26ad17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents: 8
diff changeset
90 </xml>
6
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
91 <xml name="citations">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
92 <citations>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
93 <citation type="bibtex">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
94 @misc{SAM_def,
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
95 title={Definition of SAM/BAM format},
8
71d5c34fef4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
96 url = {https://samtools.github.io/hts-specs/},}
6
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
97 </citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
98 <citation type="doi">10.1093/bioinformatics/btp352</citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
99 <citation type="doi">10.1093/bioinformatics/btr076</citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
100 <citation type="doi">10.1093/bioinformatics/btr509</citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
101 <citation type="bibtex">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
102 @misc{Danecek_et_al,
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
103 Author={Danecek, P., Schiffels, S., Durbin, R.},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
104 title={Multiallelic calling model in bcftools (-m)},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
105 url = {http://samtools.github.io/bcftools/call-m.pdf},}
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
106 </citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
107 <citation type="bibtex">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
108 @misc{Durbin_VCQC,
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
109 Author={Durbin, R.},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
110 title={Segregation based metric for variant call QC},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
111 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
112 </citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
113 <citation type="bibtex">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
114 @misc{Li_SamMath,
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
115 Author={Li, H.},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
116 title={Mathematical Notes on SAMtools Algorithms},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
117 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
118 </citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
119 <citation type="bibtex">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
120 @misc{SamTools_github,
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
121 title={SAMTools GitHub page},
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
122 url = {https://github.com/samtools/samtools},}
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
123 </citation>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
124 </citations>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
125 </xml>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
126 <xml name="version_command">
8
71d5c34fef4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
127 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
6
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
128 </xml>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
129 <xml name="stdio">
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
130 <stdio>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
131 <exit_code range="1:" level="fatal" description="Error" />
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
132 </stdio>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
133 </xml>
191cec7b989b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
diff changeset
134 </macros>