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annotate samtools_cram_to_bam.xml @ 1:d459230531aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:46:47 -0400
parents 0637018367e0
children a744bb7196a2
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0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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2 <description>convert CRAM alignments to BAM format</description>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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4 <macros>
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5 <import>macros.xml</import>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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6 </macros>
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7 <expand macro="requirements"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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11 <command><![CDATA[
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12 #if str( $input_alignment.metadata.cram_index ) != "None":
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 ln -f -s '${input_alignment.metadata.cram_index}' '${input_alignment}.crai' &&
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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14 #end if
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16 #if $reference_source.reference_source_selector == 'history':
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 #set ref_fa = 'ref.fa'
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 ln -s '${reference_source.input_reference}' ref.fa &&
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 #else:
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20 #set ref_fa = str( $reference_source.input_reference.fields.path )
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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21 #end if
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22
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 samtools view
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24 #if $parameter_regions.target_region == "regions_bed_file"
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 -L '${parameter_regions.regions_bed_file}'
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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26 #end if
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27 -@ \${GALAXY_SLOTS:-2}
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 -b
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29 -T '$ref_fa'
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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30 -o '$output_alignment'
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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31 '$input_alignment'
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32 #if $parameter_regions.target_region == "region"
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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33 '${parameter_regions.region_string}'
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34 #end if
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35 ]]></command>
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36
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37 <inputs>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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38 <param name="input_alignment" type="data" format="cram" label="CRAM alignment file"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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39 <conditional name="reference_source">
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40 <param name="reference_source_selector" type="select" label="Load reference genome from">
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41 <option value="cached">Local cache</option>
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42 <option value="history">History</option>
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43 </param>
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44 <when value="cached">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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45 <param name="input_reference" type="select" label="Reference genome">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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46 <options from_data_table="fasta_indexes">
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47 <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" />
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48 </options>
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49 <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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50 </param>
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51 </when>
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52 <when value="history">
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53 <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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54 </when>
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55 </conditional>
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56 <conditional name="parameter_regions">
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57 <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
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58 <option value="entire_input_file">Entire BAM alignment file</option>
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59 <option value="region">Specific region</option>
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60 <option value="regions_bed_file">List of specific regions (BED file)</option>
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61 </param>
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62 <when value="entire_input_file" />
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63 <when value="region">
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64 <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" />
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65 </when>
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66 <when value="regions_bed_file">
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67 <param name="regions_bed_file" argument="-L" type="data" format="bed" label="Only include reads overlapping this BED file" />
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68 </when>
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69 </conditional>
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70 </inputs>
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71
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72 <outputs>
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73 <data name="output_alignment" format="bam" label="$tool.name on ${on_string}.bam"></data>
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74 </outputs>
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75
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76 <tests>
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77 <test>
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78 <param name="input_alignment" value="test.cram" ftype="cram" />
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79 <param name="reference_source_selector" value="history" />
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80 <param name="input_reference" value="test.fa" />
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81
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82 <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
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83 </test>
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84 <test>
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85 <param name="input_alignment" value="test.cram" ftype="cram" />
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86 <param name="reference_source_selector" value="history" />
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87 <param name="input_reference" value="test.fa" />
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88 <param name="target_region" value="region" />
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89 <param name="region_string" value="CHROMOSOME_I" />
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90
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91 <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
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92 </test>
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93 <test>
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94 <param name="input_alignment" value="test.cram" ftype="cram" />
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95 <param name="reference_source_selector" value="history" />
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96 <param name="input_reference" value="test.fa" />
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97 <param name="target_region" value="regions_bed_file" />
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98 <param name="regions_bed_file" value="test.bed" ftype="bed" />
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99
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100 <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
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101 </test>
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102 <test>
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103 <param name="input_alignment" value="test2.cram" dbkey="equCab2" ftype="cram" />
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104 <param name="reference_source_selector" value="cached" />
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105 <param name="input_reference" value="equCab2chrM" />
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106 <param name="target_region" value="entire_input_file" />
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107 <output name="output_alignment" file="sam_to_bam_out2.bam" compare="sim_size" delta="250" />
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108 </test>
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109 </tests>
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110
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111 <help><![CDATA[
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112 **What this tool does**
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113
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114 Converts alignments from the CRAM format to the BAM format using the ``samtools view`` command.
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115 ]]></help>
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116 <expand macro="citations"/>
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117 </tool>