Mercurial > repos > iuc > samtools_bam_to_cram

annotate samtools_bam_to_cram.xml @ 7:b5386f2f01e7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:21:31 +0000
parents 6c790feb4215
children
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7
b5386f2f01e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
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1 <tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>convert BAM alignments to CRAM 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
f11c1dd0b4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit fdc0553f8451316c1f0b63488db3ef250e99b3ad
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11 <command><![CDATA[
2
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12 @ADDTHREADS@
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13 @PREPARE_FASTA_IDX@
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14 @PREPARE_IDX@
1
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15
0
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16 samtools view
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17 #if $parameter_regions.target_region == "regions_bed_file"
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18 -L '${parameter_regions.regions_bed_file}'
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19 #end if
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20
2
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21 -@ \$addthreads
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22 -C
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23 -h
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24 -o '${output_alignment}'
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25 -T "\$reffa"
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26 -t "\$reffai"
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27 --output-fmt-option no_ref
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28 infile
0
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29
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30 #if $parameter_regions.target_region == "region"
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31 '${parameter_regions.region_string}'
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32 #end if
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33 ]]></command>
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34
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35 <inputs>
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36 <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
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37 <expand macro="mandatory_reference" argument="-t"/>
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38 <conditional name="parameter_regions">
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39 <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
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40 <option value="entire_input_file">Entire BAM alignment file</option>
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41 <option value="region">Specific region</option>
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42 <option value="regions_bed_file">List of specific regions (BED file)</option>
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43 </param>
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44 <when value="entire_input_file" />
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45 <when value="region">
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46 <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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47 </when>
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48 <when value="regions_bed_file">
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49 <param name="regions_bed_file" argument="-L" type="data" format="bed"
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50 label="Only include reads overlapping this BED file" />
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51 </when>
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52 </conditional>
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53 </inputs>
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54
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55 <outputs>
1
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56 <data name="output_alignment" format="cram" label="$tool.name on ${on_string}.cram"></data>
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="input" value="test.bam" ftype="bam" />
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62 <param name="addref_select" value="history" />
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63 <param name="ref" value="test.fa" />
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64 <param name="target_region" value="entire_input_file" />
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65 <output name="output_alignment" file="test_bam.cram" ftype="cram" compare="sim_size" delta="250" />
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66 </test>
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67 <test>
2
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68 <param name="input" value="test.sam" ftype="sam" />
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69 <param name="addref_select" value="history" />
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70 <param name="ref" value="test.fa" />
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71 <param name="target_region" value="entire_input_file" />
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72 <output name="output_alignment" file="test_sam.cram" ftype="cram" compare="sim_size" delta="250" />
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73 </test>
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74 <test>
2
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75 <param name="input" value="test.bam" ftype="bam" />
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76 <param name="addref_select" value="history" />
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77 <param name="ref" value="test.fa" />
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78 <param name="target_region" value="region" />
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79 <param name="region_string" value="CHROMOSOME_I" />
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80 <output name="output_alignment" file="test_chr1.cram" ftype="cram" compare="sim_size" delta="250" />
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81 </test>
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82 <test>
2
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83 <param name="input" value="test.bam" ftype="bam" />
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84 <param name="addref_select" value="history" />
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85 <param name="ref" value="test.fa" />
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86 <param name="target_region" value="regions_bed_file" />
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87 <param name="regions_bed_file" value="test.bed" ftype="bed" />
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88 <output name="output_alignment" file="test_regions.cram" ftype="cram" compare="sim_size" delta="250" />
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89 </test>
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90 <test>
2
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91 <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
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92 <param name="addref_select" value="cached" />
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93 <param name="ref" value="equCab2chrM" />
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94 <param name="target_region" value="entire_input_file" />
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95 <output name="output_alignment" file="test2.cram" ftype="cram" compare="sim_size" delta="250" />
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96 </test>
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97 </tests>
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98
1
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99 <help><![CDATA[
0
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100 **What this tool does**
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101
1
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102 Converts alignments from the BAM format to the CRAM format using the ``samtools view`` command.
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103 The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient.
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104 ]]></help>
0
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105
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106 <expand macro="citations" />
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107 </tool>