Mercurial > repos > devteam > samtools_phase
annotate samtools_phase.xml @ 5:2311187710fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
---|---|
date | Tue, 09 May 2017 11:16:22 -0400 |
parents | c21cb56fbbbc |
children | dd8305e4e58e |
rev | line source |
---|---|
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
1 <tool id="samtools_phase" name="Call and phase" version="2.0.1"> |
0 | 2 <description>heterozygous SNPs</description> |
3
c21cb56fbbbc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
3 <macros> |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
4 <import>macros.xml</import> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
5 </macros> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
6 <expand macro="requirements"/> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
7 <expand macro="stdio"/> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
8 <expand macro="version_command"/> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
9 <command><![CDATA[ |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
10 samtools phase -b phase_wrapper |
0 | 11 #if str($option_set.option_sets) == 'advanced': |
12 ${option_set.ignore_chimeras} | |
13 -k $option_set.block_length | |
14 -q $option_set.min_het | |
15 -Q $option_set.min_bq | |
16 -D $option_set.read_depth | |
17 ${option_set.drop_ambiguous} | |
18 #else | |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
19 -k 13 |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
20 -q 37 |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
21 -Q 13 |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
22 -D 256 |
0 | 23 #end if |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
24 '$input_bam' > '$phase_sets' |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
25 ]]></command> |
0 | 26 <inputs> |
27 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> | |
28 <conditional name="option_set"> | |
29 <param name="option_sets" type="select" label="Phase parameters"> | |
30 <option value="default">Use defaults</option> | |
31 <option value="advanced">Advanced options</option> | |
32 </param> | |
33 <when value="default" /> | |
34 <when value="advanced"> | |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" /> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" /> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" /> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> |
0 | 41 </when> |
42 </conditional> | |
43 </inputs> | |
44 <outputs> | |
45 <data format="txt" name="phase_sets" /> | |
46 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" /> | |
47 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" /> | |
48 <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" /> | |
49 </outputs> | |
50 <tests> | |
51 <test> | |
52 <param name="option_sets" value="default" /> | |
53 <param name="input_bam" value="samtools_phase_in_1.bam" /> | |
54 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" /> | |
55 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" /> | |
56 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" /> | |
57 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
58 </test> | |
59 <test> | |
60 <param name="input_bam" value="samtools_phase_in_2.bam" /> | |
61 <param name="option_sets" value="advanced" /> | |
62 <param name="option_set|block_length" value="13" /> | |
63 <param name="option_set|min_het" value="37" /> | |
64 <param name="option_set|min_bq" value="13" /> | |
65 <param name="option_set|read_depth" value="256" /> | |
66 <param name="option_set|ignore_chimeras" value="false" /> | |
67 <param name="option_set|drop_ambiguous" value="true" /> | |
68 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" /> | |
69 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" /> | |
70 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" /> | |
71 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
72 </test> | |
73 <test> | |
74 <param name="input_bam" value="samtools_phase_in_2.bam" /> | |
75 <param name="option_sets" value="advanced" /> | |
76 <param name="option_set|block_length" value="13" /> | |
77 <param name="option_set|min_het" value="37" /> | |
78 <param name="option_set|min_bq" value="13" /> | |
79 <param name="option_set|read_depth" value="256" /> | |
80 <param name="option_set|ignore_chimeras" value="true" /> | |
81 <param name="option_set|drop_ambiguous" value="false" /> | |
82 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" /> | |
83 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" /> | |
84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" /> | |
85 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
86 </test> | |
87 </tests> | |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
88 <help><![CDATA[ |
0 | 89 **What it does** |
90 | |
5
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
91 Call and phase heterozygous SNPs. |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
92 ]]></help> |
2311187710fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
3
diff
changeset
|
93 <expand macro="citations"/> |
0 | 94 </tool> |