Mercurial > repos > iuc > samtools_view
comparison macros.xml @ 10:350bbc5c2ffd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:18:32 +0000 |
| parents | b01db2684fa5 |
| children | c370440f901e |
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| 9:b72793637686 | 10:350bbc5c2ffd |
|---|---|
| 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 is mapped to the reverse strand of the reference</option> | 135 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> |
| 85 <option value="32">Mate is mapped to the reverse strand of the reference</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 of the 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">Alignment is supplementary</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 |