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annotate samtools_merge.xml @ 3:36677f429310 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 5cb103832529f17e5c72e7f122758c13519fbe5e
author iuc
date Mon, 15 Aug 2022 09:18:27 +0000
parents b40e2d865d52
children 65a38e8c8e2a
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36677f429310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 5cb103832529f17e5c72e7f122758c13519fbe5e
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1 <tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
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2 <description>merge multiple sorted alignment files</description>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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3 <macros>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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4 <import>macros.xml</import>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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5 </macros>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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6 <expand macro="requirements"/>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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9 <command><![CDATA[
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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10 @ADDTHREADS@
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8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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11 ## prepare input (sort sam, link other), determine input ordering
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740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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12 ## and check for consistent input ordering
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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13 #set sortby=''
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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14 #for $i, $bam in enumerate( $bamfiles ):
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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15 #if $bam.is_of_type('sam', 'cram', ):
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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16 samtools sort
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8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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17 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
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740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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18 -O sam
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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19 -o ${i}.sam
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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20 '$bam' &&
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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21 #else:
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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22 ln -s '$bam' ${i}.sam &&
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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23 #end if
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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24 #if ($sortby=='coord' or $sortby=='') and $bam.is_of_type('sam','bam','cram'):
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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25 #set sortby='coord'
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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26 #else if ($sortby=='name' or $sortby=='') and $bam.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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27 #set $sortby='name'
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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28 #else:
1
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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29 >&2 echo "inconsistently sorted input" &&
0
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30 exit 1 &&
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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31 #end if
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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32 #end for
1
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33 #if $bed_file
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34 #for $i, $bam in enumerate( $bamfiles ):
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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35 samtools index ${i}.sam &&
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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36 #end for
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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37 #end if
0
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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38 samtools merge
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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39 -@ \$addthreads
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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40 -s $seed
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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41 ## TODO force overwrite seems necessay (but I do not understand why ...)
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42 -f
0
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43 ## Galaxy provides only default compression
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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44 ## #if $compression == 'levelone'
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45 ## -1
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46 ## #else if $compression == 'uncompressed'
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47 ## -u
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48 ## #end if
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49 #if str($headerbam) != 'None'
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50 -h '$headerbam'
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51 #end if
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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52 #if $sortby=='name'
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53 -n
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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54 #end if
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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55 ## TODO since galaxy can't represent this as data type at the moment this option is unsupported
1
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56 ## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
0
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57 #if str($region) != ''
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58 -R '$region'
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59 #end if
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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60 ## Attach an RG tag to each alignment. The tag value is inferred from file names.
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61 ## -r
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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62 ## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
1
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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63 #if $bed_file:
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64 -L '$bed_file'
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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65 #end if
0
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66 $idrg
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67 $idpg
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68 $output
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69 #for $i, $bam in enumerate( $bamfiles ):
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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70 ${i}.sam
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71 #end for
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72 ]]></command>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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73 <inputs>
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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74 <param name="bamfiles" type="data" format="sam,bam,cram" multiple="true" optional="false" label="Alignments in BAM format" help="Sets of aligned reads." />
1
8890e2d4c068 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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75 <param name="bed_file" type="data" optional="true" format="bed" label="Merge only reads overlapping the specified regions in the BED file" />
0
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76 <param name="region" type="text" optional="true" argument="-n" label="Merge files in a region" help="Merge files in the specified region indicated by a string" />
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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77 <param name="headerbam" type="data" format="sam,bam" argument="-h" multiple="false" optional="true" label="File to take @headers from" help="Use the lines of FILE as `@' headers to be copied to out.bam, replacing any header lines that would otherwise be copied from in1.bam. (FILE is actually in SAM format, though any alignment records it may contain are ignored.)" />
740ce0a18f0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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78 <param name="idrg" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Make @RG headers unique" help="When several input files contain @RG headers with the same ID, emit only one of them (namely, the header line from the first file we find that ID in) to the merged output file. Combining these similar headers is usually the right thing to do when the files being merged originated from the same file. Without -c, all @RG headers appear in the output file, with random suffices added to their IDs where necessary to differentiate them." />
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79 <param name="idpg" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Make @PG headers unique" help="Similarly, for each @PG ID in the set of files to merge, use the @PG line of the first file we find that ID in rather than adding a suffix to differentiate similar IDs." />
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80 <param name="seed" type="integer" argument="-s" value="1" label="random seed" />
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81 <!-- compression options are not accessible in galaxy
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82 <param name="compression" type="select" label="Advanced compression options" help="Select advanced compression options">
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83 <option value="default" selected="true">default</option>
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84 <option value="levelone">Use zlib compression level 1</option>
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85 <option value="uncompressed">Uncompressed output</option>
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86 </param>-->
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87 </inputs>
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88 <outputs>
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89 <data name="output" format="bam" />
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90 </outputs>
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91 <tests>
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92 <!--tests and data extracted from
0
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93 https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl
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94 https://github.com/samtools/samtools/tree/develop/test/merge -->
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95 <!-- Merge 1 - Standard 3 file SAM merge all presented on the command line (only checks for similar size, because generated header info differs) -->
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96 <test>
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97 <param name="bamfiles" value="test_input_1_a.sam,test_input_1_b.sam,test_input_1_c.sam" />
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98 <output name="output" file="1.merge.expected.bam" ftype="bam" lines_diff="16" />
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99 </test>
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100 <!-- Merge 2 - Standard 3 file BAM merge all files presented on the command line -->
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101 <test>
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102 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam,test_input_1_c.bam" />
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103 <output name="output" file="2.merge.expected.bam" ftype="bam" lines_diff="16" />
0
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104 </test>
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105 <!-- Merge 3 - 1 file BAM merge with file presented on the command line -->
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106 <test>
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107 <param name="bamfiles" value="test_input_1_b.bam" />
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108 <output name="output" file="3.merge.expected.bam" ftype="bam" lines_diff="16" />
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109 </test>
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110 <!--Merge 4 - merge all presented on the command line, combine PG and RG rather than dedup -->
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111 <test>
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112 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam" />
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113 <param name="idrg" value="-c" />
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114 <param name="idpg" value="-p" />
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115 <output name="output" file="4.merge.expected.bam" ftype="bam" lines_diff="16" />
0
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116 </test>
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117 <!-- Merge 5 - ID and SN with regex in them (probably not necessary for the galaxy tool because just different input) -->
0
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118 <test>
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119 <param name="bamfiles" value="test_input_1_a_regex.sam,test_input_1_b_regex.sam" />
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120 <output name="output" file="5.merge.expected.bam" ftype="bam" lines_diff="16" />
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121 </test>
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122 <!-- Merge 6 - Merging with bedfile -->
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123 <test>
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124 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam,test_input_1_c.bam" />
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125 <param name="bed_file" value="test_input_1_a.bed" />
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126 <output name="output" file="6.merge.expected.bam" ftype="bam" lines_diff="16" />
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127 </test>
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128 <!--Merge - 3 file SAM merge all presented on the command line override IDs to file names (not implemented in tool) -->
0
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129 <!-- Sort inputs by PG, then merge (not implemented, since -t not supported in the tool) -->
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130 <!-- Sort inputs by PG, then merge (name sorted) (not implemented, since -t not supported in the tool) -->
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131 </tests>
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132 <help>
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133 **What it does**
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134 Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order.
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135
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136 If a file to take @headers from is specified the @SQ headers of input files will be merged into the specified header, otherwise they will be merged into a composite header created from the input headers. If in the process of merging @SQ lines for coordinate sorted input files, a conflict arises as to the order (for example input1.bam has @SQ for a,b,c and input2.bam has b,a,c) then the resulting output file will need to be re-sorted back into coordinate order.
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137
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138 Unless the @PG/@RG headers are made unique when merging @RG and @PG records into the output header then any IDs found to be duplicates of existing IDs in the output header will have a suffix appended to them to differentiate them from similar header records from other files and the read records will be updated to reflect this.
0
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139 </help>
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140 <expand macro="citations"/>
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141 </tool>