Mercurial > repos > devteam > sam_to_bam

annotate macros.xml @ 10:cf1ffd88f895 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/sam_to_bam commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 02:17:48 -0400
parents b77f7b516b17
children 1e69848b596f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
1 <macros>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
2 <xml name="requirements">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
3 <requirements>
9
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
6
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
5 <yield/>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
6 </requirements>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
7 </xml>
9
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
8 <token name="@TOOL_VERSION@">1.9</token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
10 <token name="@PREPARE_IDX@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
11 ##prepare input and indices
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
12 ln -s '$input' infile &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
13 #if $input.is_of_type('bam'):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
14 #if str( $input.metadata.bam_index ) != "None":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
15 ln -s '${input.metadata.bam_index}' infile.bai &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
16 #else:
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
17 samtools index infile infile.bai &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
18 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
19 #elif $input.is_of_type('cram'):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
20 #if str( $input.metadata.cram_index ) != "None":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
21 ln -s '${input.metadata.cram_index}' infile.crai &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
22 #else:
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
23 samtools index infile infile.crai &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
24 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
25 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
26 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
28 ##prepare input and indices
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
29 #for $i, $bam in enumerate( $input_bams ):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
30 ln -s '$bam' '${i}' &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
31 #if $bam.is_of_type('bam'):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
32 #if str( $bam.metadata.bam_index ) != "None":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
33 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
34 #else:
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
35 samtools index '${i}' '${i}.bai' &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
36 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
37 #elif $bam.is_of_type('cram'):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
38 #if str( $bam.metadata.cram_index ) != "None":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
39 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
40 #else:
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
41 samtools index '${i}' '${i}.crai' &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
42 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
43 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
44 #end for
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
45 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
48 ##and sets the -t/-T parameters accordingly:
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
49 ##- in case of history a symbolic link is used because samtools (view) will generate
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
50 ## the index which might not be possible in the directory containing the fasta file
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
51 ##- in case of cached the absolute path is used which allows to read the cram file
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
52 ## without specifying the reference
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
53 #if $addref_cond.addref_select == "history":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
54 ln -s '${addref_cond.ref}' reference.fa &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
55 samtools faidx reference.fa &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
56 #set reffa="reference.fa"
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
57 #set reffai="reference.fa.fai"
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
58 #elif $addref_cond.addref_select == "cached":
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
59 #set reffa=str($addref_cond.ref.fields.path)
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
60 #set reffai=str($addref_cond.ref.fields.path)+".fai"
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
61 #else
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
62 #set reffa=None
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
63 #set reffai=None
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
64 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
65 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
66 <token name="@ADDTHREADS@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
69 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
70 <token name="@ADDMEMORY@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
71 ##compute the number of memory available to samtools sort (-m)
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
74 ((addmemory=addmemory*75/100)) &&
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
75 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
76 <xml name="seed_input">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
78 </xml>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
79 <xml name="flag_options">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
80 <option value="1">read is paired</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
81 <option value="2">read is mapped in a proper pair</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
82 <option value="4">read is unmapped</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
83 <option value="8">mate is unmapped</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
84 <option value="16">read reverse strand</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
85 <option value="32">mate reverse strand</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
86 <option value="64">read is the first in a pair</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
87 <option value="128">read is the second in a pair</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
88 <option value="256">alignment or read is not primary</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
89 <option value="512">read fails platform/vendor quality checks</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
90 <option value="1024">read is a PCR or optical duplicate</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
91 <option value="2048">supplementary alignment</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
92 </xml>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
93
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
94 <!-- region specification macros and tokens for tools that allow the specification
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
95 of region by bed file / space separated list of regions -->
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
96 <token name="@REGIONS_FILE@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
97 #if $cond_region.select_region == 'tab':
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
98 -t '$cond_region.targetregions'
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
99 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
100 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
101 <token name="@REGIONS_MANUAL@"><![CDATA[
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
102 #if $cond_region.select_region == 'text':
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
103 #for $i, $x in enumerate($cond_region.regions_repeat):
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
104 '${x.region}'
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
105 #end for
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
106 #end if
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
107 ]]></token>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
108 <xml name="regions_macro">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
109 <conditional name="cond_region">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
111 <option value="no" selected="True">No</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
112 <option value="text">Manualy specify regions</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
113 <option value="tab">Regions from tabular file</option>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
114 </param>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
115 <when value="no"/>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
116 <when value="text">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
117 <repeat name="regions_repeat" min="1" default="1" title="Regions">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
118 <param name="region" type="text" label="region" help="format chr:from-to">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
119 <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>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
120 </param>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
121 </repeat>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
122 </when>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
123 <when value="tab">
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
124 <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)" />
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
125 </when>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
126 </conditional>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
127 </xml>
b77f7b516b17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 8
diff changeset
128
6
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
129 <xml name="citations">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
130 <citations>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
131 <citation type="bibtex">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
132 @misc{SAM_def,
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
133 title={Definition of SAM/BAM format},
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 6
diff changeset
134 url = {https://samtools.github.io/hts-specs/},}
6
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
135 </citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
136 <citation type="doi">10.1093/bioinformatics/btp352</citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
137 <citation type="doi">10.1093/bioinformatics/btr076</citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
138 <citation type="doi">10.1093/bioinformatics/btr509</citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
139 <citation type="bibtex">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
140 @misc{Danecek_et_al,
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
141 Author={Danecek, P., Schiffels, S., Durbin, R.},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
142 title={Multiallelic calling model in bcftools (-m)},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
143 url = {http://samtools.github.io/bcftools/call-m.pdf},}
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
144 </citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
145 <citation type="bibtex">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
146 @misc{Durbin_VCQC,
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
147 Author={Durbin, R.},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
148 title={Segregation based metric for variant call QC},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
149 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
150 </citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
151 <citation type="bibtex">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
152 @misc{Li_SamMath,
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
153 Author={Li, H.},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
154 title={Mathematical Notes on SAMtools Algorithms},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
155 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
156 </citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
157 <citation type="bibtex">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
158 @misc{SamTools_github,
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
159 title={SAMTools GitHub page},
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
160 url = {https://github.com/samtools/samtools},}
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
161 </citation>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
162 </citations>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
163 </xml>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
164 <xml name="version_command">
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 6
diff changeset
165 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
6
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
166 </xml>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
167 <xml name="stdio">
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
168 <stdio>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
169 <exit_code range="1:" level="fatal" description="Error" />
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
170 </stdio>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
171 </xml>
d04d9f1c6791 Uploaded
devteam
parents:
diff changeset
172 </macros>