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annotate sam_to_bam.xml @ 8:f7a0d41036c7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:19:23 -0400
parents 881e16ad05c6
children cf1ffd88f895
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f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.1">
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2 <description>convert SAM to BAM</description>
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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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11 <command><![CDATA[
7
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12 #if $source.index_source == "history":
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13 ln -s '${source.ref_file}' input.fa &&
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14 samtools faidx input.fa &&
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15 #else
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16 ln -s '${source.index.fields.path}' input.fa &&
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17 ln -s '${source.index.fields.path}.fai' input.fa.fai &&
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18 #end if
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20 samtools view
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21 -b
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22 -@ \${GALAXY_SLOTS:-1}
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23 -t input.fa.fai '$input1' |
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25 samtools sort
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26 -O bam
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27 -@ \${GALAXY_SLOTS:-1}
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28 -o '$output1'
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29 -T temp
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30 ]]></command>
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31
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32 <inputs>
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33 <conditional name="source">
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34 <param label="Choose the source for the reference genome" name="index_source" type="select">
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35 <option value="cached">Use a built-in genome</option>
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36 <option value="history">Use a genome from the history</option>
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37 </param>
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38 <when value="cached">
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39 <param name="input1" type="data" format="sam" label="SAM file to convert">
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40 <validator type="unspecified_build" />
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41 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
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42 </param>
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43 <param name="index" type="select" label="Using reference genome">
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44 <options from_data_table="fasta_indexes">
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45 <filter column="1" key="dbkey" ref="input1" type="data_meta" />
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46 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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47 </options>
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48 </param>
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49 </when>
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50 <when value="history">
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51 <param name="input1" type="data" format="sam" label="SAM file to convert" />
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52 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM">
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58 <actions>
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59 <conditional name="source.index_source">
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60 <when value="cached">
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61 <action name="dbkey" type="metadata">
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62 <option name="source.input1" param_attribute="dbkey" type="from_param" />
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63 </action>
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64 </when>
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65 <when value="history">
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66 <action name="dbkey" type="metadata">
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67 <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
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68 </action>
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69 </when>
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70 </conditional>
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71 </actions>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="index_source" value="history" />
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77 <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
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78 <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
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79 <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" />
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80 </test>
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81 <test>
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82 <param name="index_source" value="cached" />
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83 <param name="input1" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
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84 <param name="index" value="equCab2chrM" />
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85 <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" />
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86 </test>
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87 <test>
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88 <param name="index_source" value="history" />
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89 <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
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90 <param name="ref_file" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
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91 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" />
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95 **What it does**
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96
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97 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands.
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>