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comparison macros.xml @ 3:b91e0f76afe9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit b3426aed6615742d96dfb8f7346a9e0d4e391a99-dirty
author iuc
date Sun, 14 Oct 2018 13:56:29 -0400
parents 02afb5ea2fce
children b01db2684fa5
comparison
equal deleted inserted replaced
2:02afb5ea2fce 3:b91e0f76afe9
51 ##- in case of cached the absolute path is used which allows to read the cram file 51 ##- in case of cached the absolute path is used which allows to read the cram file
52 ## without specifying the reference 52 ## without specifying the reference
53 #if $addref_cond.addref_select == "history": 53 #if $addref_cond.addref_select == "history":
54 ln -s '${addref_cond.ref}' reference.fa && 54 ln -s '${addref_cond.ref}' reference.fa &&
55 samtools faidx reference.fa && 55 samtools faidx reference.fa &&
56 #set reffa=str($addref_cond.ref) 56 #set reffa="reference.fa"
57 #set reffai="reference.fa.fai" 57 #set reffai="reference.fa.fai"
58 #elif $addref_cond.addref_select == "cached": 58 #elif $addref_cond.addref_select == "cached":
59 #set reffa=str($addref_cond.ref.fields.path) 59 #set reffa=str($addref_cond.ref.fields.path)
60 #set reffai=str($addref_cond.ref.fields.path) 60 #set reffai=str($addref_cond.ref.fields.path)+".fai"
61 #else 61 #else
62 #set reffa=None 62 #set reffa=None
63 #set reffai=None 63 #set reffai=None
64 #end if 64 #end if
65 ]]></token> 65 ]]></token>
66 <token name="@ADDTHREADS@"><![CDATA[ 66 <token name="@ADDTHREADS@"><![CDATA[
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) 67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && 68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
69 ]]></token> 69 ]]></token>
70
71 <token name="@ADDMEMORY@"><![CDATA[ 70 <token name="@ADDMEMORY@"><![CDATA[
72 ##compute the number of memory available to samtools sort (-m) 71 ##compute the number of memory available to samtools sort (-m)
73 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
74 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
75 ((addmemory=addmemory*75/100)) && 74 ((addmemory=addmemory*75/100)) &&
89 <option value="256">alignment or read is not primary</option> 88 <option value="256">alignment or read is not primary</option>
90 <option value="512">read fails platform/vendor quality checks</option> 89 <option value="512">read fails platform/vendor quality checks</option>
91 <option value="1024">read is a PCR or optical duplicate</option> 90 <option value="1024">read is a PCR or optical duplicate</option>
92 <option value="2048">supplementary alignment</option> 91 <option value="2048">supplementary alignment</option>
93 </xml> 92 </xml>
93
94 <!-- region specification macros and tokens for tools that allow the specification
95 of region by bed file / space separated list of regions -->
96 <token name="@REGIONS_FILE@"><![CDATA[
97 #if $cond_region.select_region == 'tab':
98 -t '$cond_region.targetregions'
99 #end if
100 ]]></token>
101 <token name="@REGIONS_MANUAL@"><![CDATA[
102 #if $cond_region.select_region == 'text':
103 #for $i, $x in enumerate($cond_region.regions_repeat):
104 '${x.region}'
105 #end for
106 #end if
107 ]]></token>
108 <xml name="regions_macro">
109 <conditional name="cond_region">
110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
111 <option value="no" selected="True">No</option>
112 <option value="text">Manualy specify regions</option>
113 <option value="tab">Regions from tabular file</option>
114 </param>
115 <when value="no"/>
116 <when value="text">
117 <repeat name="regions_repeat" min="1" default="1" title="Regions">
118 <param name="region" type="text" label="region" help="format chr:from-to">
119 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
120 </param>
121 </repeat>
122 </when>
123 <when value="tab">
124 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
125 </when>
126 </conditional>
127 </xml>
128
94 <xml name="citations"> 129 <xml name="citations">
95 <citations> 130 <citations>
96 <citation type="bibtex"> 131 <citation type="bibtex">
97 @misc{SAM_def, 132 @misc{SAM_def,
98 title={Definition of SAM/BAM format}, 133 title={Definition of SAM/BAM format},