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annotate samtools_calmd.xml @ 5:ed0f72810fd5 draft

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author iuc
date Tue, 09 May 2017 11:16:22 -0400
parents 609810451a80
children 3b6f46492fd8
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ed0f72810fd5 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">
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2 <description>recalculate MD/NM tags</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 #if str( $reference_source.reference_source_selector ) == "history":
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11 #set ref_fa = 'ref.fa'
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12 ln -s '${reference_source.ref_fasta}' ref.fa &&
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13 samtools faidx ref.fa &&
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14 #else:
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15 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
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16 #end if
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ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17
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18 samtools calmd
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19 #if str($option_set.option_sets) == 'advanced':
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20 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
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21 #end if
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22 -b
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23 '$input_bam'
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24 '$ref_fa'
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25 > '$calmd_output'
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26 ]]></command>
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27 <inputs>
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28 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
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29 <conditional name="reference_source">
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30 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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31 <option value="cached">Use a built-in genome</option>
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32 <option value="history">Use a genome from the history</option>
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33 </param>
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34 <when value="cached">
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35 <param name="ref_fasta" type="select" label="Using reference genome">
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36 <options from_data_table="fasta_indexes">
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37 <filter type="data_meta" column="1" key="dbkey" ref="input_bam" />
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38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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39 </options>
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40 </param>
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41 </when>
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42 <when value="history">
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43 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
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44 </when>
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45 </conditional>
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46 <conditional name="option_set">
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47 <param name="option_sets" type="select" label="Options">
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48 <option value="default">Use defaults</option>
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49 <option value="advanced">Advanced options</option>
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50 </param>
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51 <when value="default" />
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52 <when value="advanced">
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53 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
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54 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
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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" />
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56 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="option_sets" value="default" />
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66 <param name="input_bam" value="phiX.bam"/>
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67 <param name="reference_source_selector" value="history" />
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68 <param name="ref_fasta" value="phiX.fasta" />
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69 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
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70 </test>
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71 <test>
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72 <param name="option_sets" value="advanced" />
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73 <param name="change_identical" value="true" />
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74 <param name="extended_baq" value="true" />
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75 <param name="input_bam" value="phiX.bam"/>
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76 <param name="reference_source_selector" value="history" />
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77 <param name="ref_fasta" value="phiX.fasta" />
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78 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 **What it does**
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83
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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.
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85
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86 -----
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87
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88 **NM and MD tags**
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89
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90 From the SAM format specification::
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91
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92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
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93 NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
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94
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95 See references for more information about SAM format tags.
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96 ]]></help>
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97 <expand macro="citations"/>
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98 </tool>