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comparison macros.xml @ 7:10184eaa85fc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:10:41 +0000
parents 88eedb4abea0
children a53efedba9e7
comparison
equal deleted inserted replaced
6:88eedb4abea0 7:10184eaa85fc
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@TOOL_VERSION@">1.9</token> 8 <token name="@TOOL_VERSION@">1.13</token>
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> 9 <token name="@PROFILE@">20.05</token>
10 <token name="@FLAGS@"><![CDATA[
11 #set $flags = 0
12 #if $filter
13 #set $flags = sum(map(int, str($filter).split(',')))
14 #end if
15 ]]></token>
10 <token name="@PREPARE_IDX@"><![CDATA[ 16 <token name="@PREPARE_IDX@"><![CDATA[
11 ##prepare input and indices 17 ##prepare input and indices
12 ln -s '$input' infile && 18 ln -s '$input' infile &&
13 #if $input.is_of_type('bam'): 19 #if $input.is_of_type('bam'):
14 #if str( $input.metadata.bam_index ) != "None": 20 #if str( $input.metadata.bam_index ) != "None":
15 ln -s '${input.metadata.bam_index}' infile.bai && 21 ln -s '${input.metadata.bam_index}' infile.bai &&
16 #else: 22 #else:
23 samtools index infile infile.crai && 29 samtools index infile infile.crai &&
24 #end if 30 #end if
25 #end if 31 #end if
26 ]]></token> 32 ]]></token>
27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ 33 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
28 ##prepare input and indices 34 ##prepare input and indices
29 #for $i, $bam in enumerate( $input_bams ): 35 #for $i, $bam in enumerate( $input_bams ):
30 ln -s '$bam' '${i}' && 36 ln -s '$bam' '${i}' &&
31 #if $bam.is_of_type('bam'): 37 #if $bam.is_of_type('bam'):
32 #if str( $bam.metadata.bam_index ) != "None": 38 #if str( $bam.metadata.bam_index ) != "None":
33 ln -s '${bam.metadata.bam_index}' '${i}.bai' && 39 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
61 #else 67 #else
62 #set reffa=None 68 #set reffa=None
63 #set reffai=None 69 #set reffai=None
64 #end if 70 #end if
65 ]]></token> 71 ]]></token>
72
73 <xml name="optional_reference">
74 <conditional name="addref_cond">
75 <param name="addref_select" type="select" label="Use a reference sequence">
76 <help>@HELP@</help>
77 <option value="no">No</option>
78 <option value="history">Use a genome/index from the history</option>
79 <option value="cached">Use a built-in genome</option>
80 </param>
81 <when value="no"/>
82 <when value="history">
83 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
84 </when>
85 <when value="cached">
86 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
87 <options from_data_table="fasta_indexes">
88 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
89 </options>
90 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
91 </param>
92 </when>
93 </conditional>
94 </xml>
95 <xml name="mandatory_reference" token_help="" token_argument="">
96 <conditional name="addref_cond">
97 <param name="addref_select" type="select" label="Use a reference sequence">
98 <help>@HELP@</help>
99 <option value="history">Use a genome/index from the history</option>
100 <option value="cached">Use a built-in genome</option>
101 </param>
102 <when value="history">
103 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
104 </when>
105 <when value="cached">
106 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
107 <options from_data_table="fasta_indexes">
108 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
109 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
110 </options>
111 </param>
112 </when>
113 </conditional>
114 </xml>
115
116
66 <token name="@ADDTHREADS@"><![CDATA[ 117 <token name="@ADDTHREADS@"><![CDATA[
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) 118 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && 119 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
69 ]]></token> 120 ]]></token>
70 <token name="@ADDMEMORY@"><![CDATA[ 121 <token name="@ADDMEMORY@"><![CDATA[
71 ##compute the number of memory available to samtools sort (-m) 122 ##compute the number of memory available to samtools sort (-m)
72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 123 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 124 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
74 ((addmemory=addmemory*75/100)) && 125 ((addmemory=addmemory*75/100)) &&
75 ]]></token> 126 ]]></token>
76 <xml name="seed_input"> 127 <xml name="seed_input">
77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 128 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
78 </xml> 129 </xml>
79 <xml name="flag_options"> 130 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
80 <option value="1">read is paired</option> 131 <option value="1" selected="@S1@">Read is paired</option>
81 <option value="2">read is mapped in a proper pair</option> 132 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
82 <option value="4">read is unmapped</option> 133 <option value="4" selected="@S4@">Read is unmapped</option>
83 <option value="8">mate is unmapped</option> 134 <option value="8" selected="@S8@">Mate is unmapped</option>
84 <option value="16">read reverse strand</option> 135 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
85 <option value="32">mate reverse strand</option> 136 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
86 <option value="64">read is the first in a pair</option> 137 <option value="64" selected="@S64@">Read is the first in a pair</option>
87 <option value="128">read is the second in a pair</option> 138 <option value="128" selected="@S128@">Read is the second in a pair</option>
88 <option value="256">alignment or read is not primary</option> 139 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
89 <option value="512">read fails platform/vendor quality checks</option> 140 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
90 <option value="1024">read is a PCR or optical duplicate</option> 141 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
91 <option value="2048">supplementary alignment</option> 142 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
92 </xml> 143 </xml>
93 144
94 <!-- region specification macros and tokens for tools that allow the specification 145 <!-- region specification macros and tokens for tools that allow the specification
95 of region by bed file / space separated list of regions --> 146 of region by bed file / space separated list of regions -->
96 <token name="@REGIONS_FILE@"><![CDATA[ 147 <token name="@REGIONS_FILE@"><![CDATA[
97 #if $cond_region.select_region == 'tab': 148 #if $cond_region.select_region == 'tab':
98 -t '$cond_region.targetregions' 149 -t '$cond_region.targetregions'
99 #end if 150 #end if