Mercurial > repos > devteam > samtools_phase

annotate samtools_phase.xml @ 4:1e5880498f52 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/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:15:54 +0000
parents b5c3b1856370
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
1 <tool id="samtools_phase" name="Samtools phase" version="2.0.2" profile="@PROFILE@">
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
2 <description>call and phase heterozygous SNPs</description>
1
8bfe0d1616d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
3 <macros>
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
5 </macros>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
6 <expand macro="requirements"/>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
7 <expand macro="stdio"/>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
8 <expand macro="version_command"/>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
9 <command><![CDATA[
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
10 samtools phase -b phase_wrapper
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
11 #if str($option_set.option_sets) == 'advanced':
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
12 ${option_set.ignore_chimeras}
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
13 -k $option_set.block_length
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
14 -q $option_set.min_het
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
15 -Q $option_set.min_bq
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
16 -D $option_set.read_depth
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
17 ${option_set.drop_ambiguous}
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
18 #else
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
19 -k 13
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
20 -q 37
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
21 -Q 13
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
22 -D 256
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
23 #end if
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
24 '$input_bam' > '$phase_sets'
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
25 ]]></command>
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
26 <inputs>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
27 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
28 <conditional name="option_set">
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
29 <param name="option_sets" type="select" label="Phase parameters">
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
30 <option value="default">Use defaults</option>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
31 <option value="advanced">Advanced options</option>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
32 </param>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
33 <when value="default" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
34 <when value="advanced">
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
3
b5c3b1856370 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 2
diff changeset
40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
41 </when>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
42 </conditional>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
43 </inputs>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
44 <outputs>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
45 <data format="txt" name="phase_sets" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
46 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
47 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
3
b5c3b1856370 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 2
diff changeset
48 <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
49 </outputs>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
50 <tests>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
51 <test>
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
52 <param name="option_sets" value="default" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
53 <param name="input_bam" value="samtools_phase_in_1.bam" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
54 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
55 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
56 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
57 <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
58 </test>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
59 <test>
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
60 <param name="input_bam" value="samtools_phase_in_2.bam" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
61 <param name="option_sets" value="advanced" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
62 <param name="option_set|block_length" value="13" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
63 <param name="option_set|min_het" value="37" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
64 <param name="option_set|min_bq" value="13" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
65 <param name="option_set|read_depth" value="256" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
66 <param name="option_set|ignore_chimeras" value="false" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
67 <param name="option_set|drop_ambiguous" value="true" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
68 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
69 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
70 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
71 <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
72 </test>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
73 <test>
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
74 <param name="input_bam" value="samtools_phase_in_2.bam" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
75 <param name="option_sets" value="advanced" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
76 <param name="option_set|block_length" value="13" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
77 <param name="option_set|min_het" value="37" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
78 <param name="option_set|min_bq" value="13" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
79 <param name="option_set|read_depth" value="256" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
80 <param name="option_set|ignore_chimeras" value="true" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
81 <param name="option_set|drop_ambiguous" value="false" />
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
82 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
4
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
83 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" />
1e5880498f52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
85 <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" />
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
86 </test>
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
87 </tests>
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
88 <help><![CDATA[
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
89 **What it does**
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
90
2
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
91 Call and phase heterozygous SNPs.
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
92 ]]></help>
6166013090c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 1
diff changeset
93 <expand macro="citations"/>
0
cba1944e3ed0 Uploaded tool and dependency definition.
devteam
parents:
diff changeset
94 </tool>