Mercurial > repos > devteam > samtools_calmd
annotate samtools_calmd.xml @ 1:33208952b99d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
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date | Tue, 09 May 2017 11:18:11 -0400 |
parents | 1ebb4ecdc1ef |
children | e65c2cd0964c |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="samtools_calmd" name="CalMD" version="2.0.1"> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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2 <description>recalculate MD/NM tags</description> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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3 <macros> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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4 <import>macros.xml</import> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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5 </macros> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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6 <expand macro="requirements"/> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="stdio"/> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="version_command"/> |
0 | 9 <command><![CDATA[ |
10 #if str( $reference_source.reference_source_selector ) == "history": | |
11 #set ref_fa = 'ref.fa' | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 ln -s '${reference_source.ref_fasta}' ref.fa && |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 samtools faidx ref.fa && |
0 | 14 #else: |
15 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) | |
16 #end if | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 |
0 | 18 samtools calmd |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 #if str($option_set.option_sets) == 'advanced': |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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20 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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21 #end if |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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22 -b |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 '$input_bam' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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24 '$ref_fa' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 > '$calmd_output' |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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26 ]]></command> |
0 | 27 <inputs> |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> |
0 | 29 <conditional name="reference_source"> |
30 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
31 <option value="cached">Use a built-in genome</option> | |
32 <option value="history">Use a genome from the history</option> | |
33 </param> | |
34 <when value="cached"> | |
35 <param name="ref_fasta" type="select" label="Using reference genome"> | |
36 <options from_data_table="fasta_indexes"> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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37 <filter type="data_meta" column="1" key="dbkey" ref="input_bam" /> |
0 | 38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
39 </options> | |
40 </param> | |
41 </when> | |
42 <when value="history"> | |
43 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> | |
44 </when> | |
45 </conditional> | |
46 <conditional name="option_set"> | |
47 <param name="option_sets" type="select" label="Options"> | |
48 <option value="default">Use defaults</option> | |
49 <option value="advanced">Advanced options</option> | |
50 </param> | |
51 <when value="default" /> | |
52 <when value="advanced"> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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53 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" /> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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54 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" /> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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55 <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" /> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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56 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" /> |
0 | 57 </when> |
58 </conditional> | |
59 </inputs> | |
60 <outputs> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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61 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" /> |
0 | 62 </outputs> |
63 <tests> | |
64 <test> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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65 <param name="option_sets" value="default" /> |
0 | 66 <param name="input_bam" value="phiX.bam"/> |
67 <param name="reference_source_selector" value="history" /> | |
68 <param name="ref_fasta" value="phiX.fasta" /> | |
69 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> | |
70 </test> | |
71 <test> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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72 <param name="option_sets" value="advanced" /> |
0 | 73 <param name="change_identical" value="true" /> |
74 <param name="extended_baq" value="true" /> | |
75 <param name="input_bam" value="phiX.bam"/> | |
76 <param name="reference_source_selector" value="history" /> | |
77 <param name="ref_fasta" value="phiX.fasta" /> | |
78 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> | |
79 </test> | |
80 </tests> | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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81 <help><![CDATA[ |
0 | 82 **What it does** |
83 | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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84 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see SAM format reference below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. |
0 | 85 |
86 ----- | |
87 | |
88 **NM and MD tags** | |
89 | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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90 From the SAM format specification:: |
0 | 91 |
92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 | |
93 NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping | |
94 | |
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33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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95 See references for more information about SAM format tags. |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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96 ]]></help> |
33208952b99d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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97 <expand macro="citations"/> |
0 | 98 </tool> |