Mercurial > repos > iuc > samtools_cram_to_bam

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:14:11 +0000
parents 55ae400c0cc4
children
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7
974fe4f4e52b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit cd62639660bef041ba14ecff337fb98e84e75d8a
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1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>convert CRAM alignments to BAM format</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10
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11 <command><![CDATA[
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12 @ADDTHREADS@
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13 ln -s '$input' input.cram &&
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14 #if str( $input.metadata.cram_index ) != "None":
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15 ln -f -s '${input.metadata.cram_index}' input.cram.crai &&
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16 #end if
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17
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18 @PREPARE_FASTA_IDX@
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20 samtools view
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21 #if $parameter_regions.target_region == "regions_bed_file"
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22 -L '$parameter_regions.regions_bed_file'
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23 #end if
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24 -@ \$addthreads
0
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25 -b
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26 -T "\$reffa"
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27 -o '$output_alignment'
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28 input.cram
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29 #if $parameter_regions.target_region == "region"
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30 '$parameter_regions.region_string'
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31 #end if
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32 ]]></command>
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33
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34 <inputs>
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35 <param name="input" type="data" format="cram" label="CRAM alignment file"/>
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36 <expand macro="mandatory_reference" argument="-t"/>
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37 <conditional name="parameter_regions">
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38 <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
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39 <option value="entire_input_file">Entire BAM alignment file</option>
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40 <option value="region">Specific region</option>
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41 <option value="regions_bed_file">List of specific regions (BED file)</option>
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42 </param>
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43 <when value="entire_input_file" />
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44 <when value="region">
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45 <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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46 </when>
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47 <when value="regions_bed_file">
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48 <param name="regions_bed_file" argument="-L" type="data" format="bed" label="Only include reads overlapping this BED file" />
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49 </when>
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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54 <data name="output_alignment" format="bam" label="$tool.name on ${on_string}.bam"></data>
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input" value="test.cram" ftype="cram" />
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60 <param name="addref_select" value="history" />
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61 <param name="ref" value="test.fa" />
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62 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
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63 </test>
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64 <test>
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65 <param name="input" value="test.cram" ftype="cram" />
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66 <param name="addref_select" value="history" />
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67 <param name="ref" value="test.fa" />
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68 <param name="target_region" value="region" />
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69 <param name="region_string" value="CHROMOSOME_I" />
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70 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
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71 </test>
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72 <test>
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73 <param name="input" value="test.cram" ftype="cram" />
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74 <param name="addref_select" value="history" />
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75 <param name="ref" value="test.fa" />
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76 <param name="target_region" value="regions_bed_file" />
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77 <param name="regions_bed_file" value="test.bed" ftype="bed" />
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78 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
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79 </test>
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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80 <test>
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81 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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82 <param name="addref_select" value="cached" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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83 <param name="ref" value="equCab2chrM" />
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84 <param name="target_region" value="entire_input_file" />
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85 <output name="output_alignment" file="sam_to_bam_out2.bam" ftype="bam" lines_diff="4" />
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86 </test>
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87 </tests>
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88
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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89 <help><![CDATA[
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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90 **What this tool does**
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91
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92 Converts alignments from the CRAM format to the BAM format using the ``samtools view`` command.
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93 ]]></help>
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94 <expand macro="citations"/>
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95 </tool>