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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:21:53 +0000
parents d83ad701f011
children
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c701f5f96f32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@">
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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[
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12 @ADDTHREADS@
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13 @ADDMEMORY@
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14 @PREPARE_FASTA_IDX@
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16 samtools view
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17 -b
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18 -@ \$addthreads
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19 -t "\$reffai"
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20 '$input' |
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22 samtools sort
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23 -O bam
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24 -@ \$addthreads -m \$addmemory"M"
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25 -o '$output1'
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26 -T "\${TMPDIR:-.}"
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27 ]]></command>
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28
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29 <inputs>
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30 <param name="input" type="data" format="sam" label="SAM file to convert"/>
c701f5f96f32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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31 <expand macro="mandatory_reference" argument="-t"/>
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32 </inputs>
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33 <outputs>
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34 <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM">
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35 <actions>
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36 <conditional name="addref_cond.addref_select">
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37 <when value="cached">
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38 <action name="dbkey" type="metadata">
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39 <option name="input" param_attribute="dbkey" type="from_param" />
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40 </action>
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41 </when>
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42 <when value="history">
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43 <action name="dbkey" type="metadata">
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44 <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" />
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45 </action>
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46 </when>
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47 </conditional>
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48 </actions>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="addref_select" value="history" />
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54 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
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55 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
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56 <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/>
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57 </test>
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58 <test>
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59 <param name="addref_select" value="cached" />
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60 <param name="ref" value="equCab2chrM" />
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61 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
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62 <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/>
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63 </test>
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64 <test>
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65 <param name="addref_select" value="history" />
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66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
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67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
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68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
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69 </test>
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70 <test>
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71 <!-- Test direct use of bgzipped reference -->
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72 <param name="addref_select" value="history" />
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73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
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74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
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75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
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76 </test>
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77 <test>
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78 <!-- Test with simple gzipped reference, which requires decompression -->
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79 <param name="addref_select" value="history" />
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80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
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81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
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82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 **What it does**
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87
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4afb4a5f0924 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands.
4afb4a5f0924 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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89 ]]></help>
4afb4a5f0924 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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90 <expand macro="citations"/>
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91 </tool>