Mercurial > repos > iuc > samtools_view

annotate samtools_view.xml @ 1:390fc279c3e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
author iuc
date Tue, 25 Sep 2018 04:21:03 -0400
parents 5b44ef788111
children 80d8ca44f8da
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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2 <description>reformat, filter, or subsample</description>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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3 <macros>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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4 <import>macros.xml</import>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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5 </macros>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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6 <expand macro="requirements"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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7 <expand macro="stdio"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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8 <expand macro="version_command"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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9 <command><![CDATA[
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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10 @ADDTHREADS@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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11 ## prepare reference data
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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12 @PREPARE_FASTA_IDX@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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13 @PREPARE_IDX@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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14
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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15 ##call samtools view
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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16 samtools view
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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17 -@ \$addthreads
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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18
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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19 #if $outtype == 'count':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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20 -c
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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21 #elif $outtype == 'bam':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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22 -b
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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23 #elif $outtype == 'cram':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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24 -C
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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25 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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26
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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27 ## filter options (regions filter is the last parameter)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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28 #if $cond_filter.select_filter == 'yes':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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29 #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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30 -L '$cond_filter.bedfile'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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31 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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32 #if $cond_filter.cond_rg.select_rg == 'text':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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33 -r '$cond_filter.cond_rg.readgr'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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34 #else if $cond_filter.cond_rg.select_rg == 'file':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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35 -R '$cond_filter.cond_rg.rgfile'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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36 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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37 #if str($cond_filter.quality) != '' and int( $cond_filter.quality ) > 0
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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38 -q $cond_filter.quality
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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39 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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40 #if str( $cond_filter.library ) != ''
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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41 -l '$cond_filter.library'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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42 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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43 #if str( $cond_filter.cigarcons ) != ''
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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44 -m $cond_filter.cigarcons
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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46 #if str($cond_filter.inclusive_filter) != 'None':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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47 #set $filter = $cond_filter.inclusive_filter
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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48 @FLAGS@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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49 -f $flags
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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50 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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51 #if str($cond_filter.exclusive_filter) != 'None':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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52 #set $filter = $cond_filter.exclusive_filter
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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53 @FLAGS@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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54 -F $flags
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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55 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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56 #if str($cond_filter.exclusive_filter_all) != 'None':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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57 #set $filter = $cond_filter.exclusive_filter_all
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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58 @FLAGS@
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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59 -G $flags
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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60 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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61 #for $i, $s in enumerate($cond_filter.readtags)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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62 -x '${s.readtag}'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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63 #end for
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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64 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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65 #if $cond_subsample.select_subsample == 'yes':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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66 #set fraction=str($cond_subsample.subsample).split('.')[1]
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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67 #if str($cond_subsample.seed) == '':
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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68 -s "\${RANDOM}".$fraction
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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69 #else
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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70 -s $cond_subsample.seed.$fraction
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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71 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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72 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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73
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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74 ## output options
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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75 $adv_output.header
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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76 $adv_output.collapsecigar
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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77 #if $adv_output.outputpassing == 'yes'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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78 -U inv_outfile
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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79 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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80 -o outfile
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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81
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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82 ## additional reference data
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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83 #if $reffa!=None:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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84 -T '$reffa'
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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85 -t '$reffai'
1
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86 #end if
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87
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88 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
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89 #if $outtype=='cram':
0
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90 --output-fmt-option no_ref
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91 #end if
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92
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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93 infile
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94
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95 ## region filter need to be at the end
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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96 #if $cond_filter.select_filter == 'yes' and $cond_filter.cond_region.select_region == 'text':
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97 '$cond_filter.cond_region.regions'
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98 #end if
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99
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100 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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101 ## then sort the output by coordinate,
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102 #if not $input.is_of_type('bam') and $outtype == 'bam':
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103 && samtools sort
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104 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
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105 -O bam
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106 -o 'tmpsam'
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107 outfile
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108 && mv tmpsam outfile
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109 #if $adv_output.outputpassing == 'yes':
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110 && samtools sort
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111 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
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112 -O bam
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113 -o 'tmpsam'
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114 inv_outfile
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115 && mv tmpsam inv_outfile
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116 #end if
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117 #end if
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118 ]]></command>
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119 <inputs>
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120 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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121 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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122 <param name="outtype" type="select" argument="-b/-C/-c" label="Output type">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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123 <help>Select output type. In case of counts only the total number of alignments is returned. All filters are taken into account</help>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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124 <option value="sam">SAM</option>
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125 <option value="bam">BAM (-b)</option>
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126 <option value="cram">CRAM (-C)</option>
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127 <option value="count">Count of alignments (-c)</option>
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128 </param>
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129 <conditional name="cond_filter">
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130 <param name="select_filter" type="select" label="Filter alignment">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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131 <option value="yes">Yes</option>
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132 <option value="no" selected="True">No</option>
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133 </param>
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134 <when value="yes">
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135 <conditional name="cond_region">
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136 <param name="select_region" type="select" label="Filter by regions">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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137 <option value="no" selected="True">No</option>
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138 <option value="text">Manualy specify regions</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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139 <option value="bed">Regions from BED file</option>
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140 </param>
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141 <when value="no"/>
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142 <when value="text">
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143 <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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144 </when>
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145 <when value="bed">
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146 <param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." />
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147 </when>
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148 </conditional>
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149 <conditional name="cond_rg">
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150 <param name="select_rg" type="select" label="Filter by readgroup">
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151 <option value="no" selected="True">No</option>
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152 <option value="text">Single read group </option>
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153 <option value="file">Read groups from file</option>
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154 </param>
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155 <when value="no"/>
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156 <when value="text">
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157 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
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158 </when>
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159 <when value="file">
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160 <param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." />
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161 </when>
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162 </conditional>
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163 <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." />
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164 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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165 <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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166 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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167 <expand macro="flag_options" />
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168 </param>
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169 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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170 <expand macro="flag_options" />
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171 </param>
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172 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
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173 <expand macro="flag_options" />
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174 </param>
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175 <!-- TODO could also make this a text field (comma/space separated) -->
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176 <repeat name="readtags" title="Filter by read tags">
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177 <param name="readtag" type="text" argument="-x" label="Filter by read tag" help="Read tag to exclude from output."/>
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178 </repeat>
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179 </when>
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180 <when value="no"/>
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181 </conditional>
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182 <conditional name="cond_subsample">
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183 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
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184 <option value="yes">Yes</option>
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185 <option value="no" selected="True">No</option>
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186 </param>
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187 <when value="yes">
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188 <param name="subsample" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
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189 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
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190 </when>
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191 <when value="no"/>
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192 </conditional>
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193 <conditional name="addref_cond">
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194 <param name="addref_select" type="select" label="Reference data">
1
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195 <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help>
0
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196 <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option>
1
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197 <option value="history">Use a genome/index from the history (-t/-T)</option>
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198 <option value="cached">Use a built-in genome (-t/-T)</option>
0
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199 </param>
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200 <when value="no"/>
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201 <when value="history">
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202 <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
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203 </when>
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204 <when value="cached">
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205 <param name="ref" type="select" label="Using reference genome">
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206 <options from_data_table="fasta_indexes">
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207 <filter column="1" key="dbkey" ref="input" type="data_meta" />
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208 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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209 </options>
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210 </param>
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211 </when>
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212 </conditional>
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213 <section name="adv_output" title="Output Options" expanded="false">
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214 <param name="header" type="select" argument="-h/-H" label="Header options">
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215 <option value="-h" selected="True">Include header in SAM output (-h)</option>
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216 <option value="-H">Return header only (-H)</option>
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217 <option value="">Exclude header</option>
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218 </param>
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219 <param name="outputpassing" type="boolean" argument="-U" truevalue="yes" falsevalue="no" checked="false" label="Output alignments not passing the filter" help="Write alignments that are not selected by the various filter options to an extra data set. When this option is used, all alignments (or all alignments intersecting the regions specified) are written to either the output data set or this extra output data set, but never both." />
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220 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
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221 </section>
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222 </inputs>
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223 <outputs>
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224 <!-- TODO do I need an action for dbkey? -->
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225 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
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226 <filter>outtype != 'count'</filter>
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227 <!-- TODO is change_format deprecated? how can I modify the type for the different bam types? -->
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228 <change_format>
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229 <when input="outtype" value="sam" format="sam" />
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230 <when input="outtype" value="bam" format="bam" />
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231 <when input="outtype" value="cram" format="cram" />
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232 </change_format>
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233 </data>
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234 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments">
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235 <filter>adv_output['outputpassing'] == 'yes' and outtype != 'count'</filter>
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236 <change_format>
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237 <when input="outtype" value="sam" format="sam" />
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238 <when input="outtype" value="bam" format="bam" />
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239 <when input="outtype" value="cram" format="cram" />
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240 </change_format>
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241 </data>
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242 <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts">
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243 <filter>outtype == 'count'</filter>
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244 </data>
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245 </outputs>
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diff changeset
246 <tests>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
247 <!-- sam to bam (copied from the sam_to_bam tool) -->
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
248 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
249 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
250 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
251 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
252 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
253 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
254 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
255 <output name="outputsam" ftype="bam" file="sam_to_bam_out1.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
256 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
257 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
258 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
259 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
260 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
261 <param name="addref_select" value="cached" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
262 <param name="ref" value="equCab2chrM" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
263 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
264 <output name="outputsam" ftype="bam" file="sam_to_bam_out2.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
265 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
266 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
267 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
268 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
269 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
270 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
271 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
272 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
273 <output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
274 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
275 <!-- bam to cram + region filter (adapted from bam_to_cram tool)-->
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
276 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
277 <param name="input" value="test.bam" ftype="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
278 <param name="outtype" value="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
279 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
280 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
281 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
282 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
283 <conditional name="cond_filter">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
284 <param name="select_filter" value="yes" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
285 <conditional name="cond_region">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
286 <param name="select_region" value="no"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
287 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
288 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
289 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
290 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
291 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
292 <param name="input" value="test.sam" ftype="sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
293 <param name="outtype" value="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
294 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
295 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
296 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
297 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
298 <conditional name="cond_filter">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
299 <param name="select_filter" value="yes" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
300 <conditional name="cond_region">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
301 <param name="select_region" value="no"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
302 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
303 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
304 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
305 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
306 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
307 <param name="input" value="test.bam" ftype="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
308 <param name="outtype" value="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
309 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
310 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
311 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
312 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
313 <conditional name="cond_filter">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
314 <param name="select_filter" value="yes" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
315 <conditional name="cond_region">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
316 <param name="select_region" value="text"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
317 <param name="regions" value="CHROMOSOME_I" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
318 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
319 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
320 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
321 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
322 <!-- bam to sam + header options (adapted from bam_to_sam tool)-->
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
323 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
324 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
325 <param name="outtype" value="sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
326 <param name="header" value="-h" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
327 <output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
328 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
329 <test>
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330 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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331 <param name="outtype" value="sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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332 <param name="header" value="-H" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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333 <output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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334 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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335 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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336 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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337 <param name="outtype" value="sam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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338 <param name="header" value="" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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339 <output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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340 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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341 <!-- cram to bam + region (adapted from cram_to_bam tool)-->
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342 <test>
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343 <param name="input" value="test.cram" ftype="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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344 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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345 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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346 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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347 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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348 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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349 <output name="outputsam" file="test.bam" ftype="bam" />
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350 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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351 <test>
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352 <param name="input" value="test.cram" ftype="cram" />
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353 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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354 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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355 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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356 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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357 </conditional>
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358 <param name="target_region" value="region" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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359 <param name="region_string" value="CHROMOSOME_I" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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360 <output name="outputsam" file="test.bam" ftype="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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361 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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362 <test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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363 <param name="input" value="test.cram" ftype="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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364 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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diff changeset
365 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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366 <param name="addref_select" value="history" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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367 <param name="ref" value="test.fa" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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368 </conditional>
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369 <param name="target_region" value="regions_bed_file" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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370 <param name="regions_bed_file" value="test.bed" ftype="bed" />
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371
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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372 <output name="outputsam" file="test.bam" ftype="bam" />
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373 </test>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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374 <test>
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375 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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376 <param name="outtype" value="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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diff changeset
377 <conditional name="addref_cond">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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378 <param name="addref_select" value="cached" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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379 <param name="ref" value="equCab2chrM" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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380 </conditional>
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381 <conditional name="cond_region">
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382 <param name="select_region" value="no"/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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383 </conditional>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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384 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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385 </test>
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386 </tests>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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387 <help>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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388 **What it does**
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389
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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390 Samtools view can:
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391
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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392 1. filter alignments according to various criteria
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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393 2. convert between alignment formats (SAM, BAM, CRAM)
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394
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395 With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
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396
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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397 **Alignment format conversion**
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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398
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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399 Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type".
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400
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401 .. class:: infomark
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402
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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403 samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed.
1
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404 CRAM is (intended as a primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM.
390fc279c3e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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405 But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM).
0
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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406
1
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407 The Galaxy tool **currently generates only CRAM without reference sequence**.
0
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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408
1
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409 For reference based CRAM input the correct refernce sequence needs to be specified.
0
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410
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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411 **Filtering alignments**
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412
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413 samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments.
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414
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415
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417 **Filtering by regions**
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418
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419 You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
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420
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421 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.
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422
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423 Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
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424
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425 Examples of region specifications:
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426
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427 - chr1 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
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428 - chr2:1000000 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
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429 - chr3:1000-2000 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
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430 - '*' Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.)
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431 - . Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
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432
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433 **Filtering by quality**
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434
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435 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignemnt. Note that aligners do not follow a consistent definition.
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436
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437 The -x, -B, and -s options modify the data which is contained in each alignment.
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438 </help>
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439 <expand macro="citations"/>
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440 </tool>