Mercurial > repos > devteam > samtools_calmd
comparison samtools_calmd.xml @ 3:609810451a80 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:54:20 -0400 |
| parents | 787d6c86c6ea |
| children | ed0f72810fd5 |
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| 2:787d6c86c6ea | 3:609810451a80 |
|---|---|
| 1 <tool id="samtools_calmd" name="Recalculate" version="1.0.1"> | 1 <tool id="samtools_calmd" name="CalMD" version="2.0"> |
| 2 <description>MD/NM tags and '=' bases</description> | 2 <description>recalculate MD/NM tags</description> |
| 3 <requirements> | 3 <macros> |
| 4 <requirement type="package" version="1.1">samtools</requirement> | 4 <import>macros.xml</import> |
| 5 </requirements> | 5 </macros> |
| 6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> | 6 <expand macro="requirements"></expand> |
| 7 <expand macro="stdio"></expand> | |
| 8 <expand macro="version_command"></expand> | |
| 7 <command><![CDATA[ | 9 <command><![CDATA[ |
| 8 #if str( $reference_source.reference_source_selector ) == "history": | 10 #if str( $reference_source.reference_source_selector ) == "history": |
| 9 #set ref_fa = 'ref.fa' | 11 #set ref_fa = 'ref.fa' |
| 10 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && | 12 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && |
| 11 #else: | 13 #else: |
| 15 #if str($option_set.option_sets) == 'advanced': | 17 #if str($option_set.option_sets) == 'advanced': |
| 16 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq | 18 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq |
| 17 #end if | 19 #end if |
| 18 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> | 20 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> |
| 19 </command> | 21 </command> |
| 20 <stdio> | |
| 21 <exit_code range="1:" level="fatal" description="Error" /> | |
| 22 </stdio> | |
| 23 <inputs> | 22 <inputs> |
| 24 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> | 23 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> |
| 25 <conditional name="reference_source"> | 24 <conditional name="reference_source"> |
| 26 <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA"> | 25 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
| 27 <option value="cached">Locally cached</option> | 26 <option value="cached">Use a built-in genome</option> |
| 28 <option value="history">History</option> | 27 <option value="history">Use a genome from the history</option> |
| 29 </param> | 28 </param> |
| 30 <when value="cached"> | 29 <when value="cached"> |
| 31 <param name="ref_fasta" type="select" label="Using reference genome"> | 30 <param name="ref_fasta" type="select" label="Using reference genome"> |
| 32 <options from_data_table="fasta_indexes"> | 31 <options from_data_table="fasta_indexes"> |
| 33 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> | 32 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> |
| 44 <option value="default">Use defaults</option> | 43 <option value="default">Use defaults</option> |
| 45 <option value="advanced">Advanced options</option> | 44 <option value="advanced">Advanced options</option> |
| 46 </param> | 45 </param> |
| 47 <when value="default" /> | 46 <when value="default" /> |
| 48 <when value="advanced"> | 47 <when value="advanced"> |
| 49 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" /> | 48 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/> |
| 50 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" /> | 49 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/> |
| 51 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" /> | 50 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/> |
| 52 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" /> | 51 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/> |
| 53 </when> | 52 </when> |
| 54 </conditional> | 53 </conditional> |
| 55 </inputs> | 54 </inputs> |
| 56 <outputs> | 55 <outputs> |
| 57 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> | 56 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> |
| 58 </outputs> | 57 </outputs> |
| 59 <tests> | 58 <tests> |
| 60 <test> | 59 <test> |
| 61 <param name="option_sets" value="default" /> | 60 <param name="option_sets" value="default" /> |
| 62 <param name="input_bam" value="phiX.bam" dbkey="phiX" /> | 61 <param name="input_bam" value="phiX.bam"/> |
| 63 <param name="reference_source|reference_source_selector" value="history" /> | 62 <param name="reference_source_selector" value="history" /> |
| 64 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" /> | 63 <param name="ref_fasta" value="phiX.fasta" /> |
| 65 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> | |
| 66 </test> | |
| 67 <!-- Using the test-data-repo's phiX.fa should produce the same output. --> | |
| 68 <test> | |
| 69 <param name="option_sets" value="default" /> | |
| 70 <param name="input_bam" value="phiX.bam" dbkey="phiX" /> | |
| 71 <param name="reference_source|reference_source_selector" value="cached" /> | |
| 72 <param name="ref_fasta" value="phiX" /> | |
| 73 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> | 64 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> |
| 74 </test> | 65 </test> |
| 75 <test> | 66 <test> |
| 76 <param name="option_sets" value="advanced" /> | 67 <param name="option_sets" value="advanced" /> |
| 77 <param name="change_identical" value="true" /> | 68 <param name="change_identical" value="true" /> |
| 78 <param name="extended_baq" value="true" /> | 69 <param name="extended_baq" value="true" /> |
| 79 <param name="input_bam" value="phiX.bam" dbkey="phiX" /> | 70 <param name="input_bam" value="phiX.bam"/> |
| 80 <param name="reference_source|reference_source_selector" value="history" /> | 71 <param name="reference_source_selector" value="history" /> |
| 81 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" /> | 72 <param name="ref_fasta" value="phiX.fasta" /> |
| 82 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> | |
| 83 </test> | |
| 84 <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. --> | |
| 85 <test> | |
| 86 <param name="option_sets" value="advanced" /> | |
| 87 <param name="change_identical" value="true" /> | |
| 88 <param name="extended_baq" value="true" /> | |
| 89 <param name="input_bam" value="phiX.bam" dbkey="phiX" /> | |
| 90 <param name="reference_source|reference_source_selector" value="cached" /> | |
| 91 <param name="ref_fasta" value="phiX" /> | |
| 92 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> | 73 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> |
| 93 </test> | 74 </test> |
| 94 </tests> | 75 </tests> |
| 95 <help> | 76 <help> |
| 96 **What it does** | 77 **What it does** |
| 97 | 78 |
| 98 Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. | 79 Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce 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. The command has the following options:: |
| 99 | 80 |
| 100 ------ | 81 -e change identical bases to '=' |
| 82 -A modify the quality string | |
| 83 -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) | |
| 84 -E extended BAQ for better sensitivity but lower specificity | |
| 85 | |
| 86 ----- | |
| 101 | 87 |
| 102 **Citation** | 88 **NM and MD tags** |
| 103 | 89 |
| 104 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | 90 From SAM format specification:: |
| 105 | 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 | |
| 95 See refernces for more information about SAM format tags. | |
| 106 | 96 |
| 107 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | 97 </help> |
| 108 | 98 <expand macro="citations"></expand> |
| 109 </help> | |
| 110 </tool> | 99 </tool> |