comparison macros.xml @ 20:f4d5237a84f6 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
author bgruening
date Mon, 18 Mar 2024 09:35:41 +0000
parents 15cd64d7c58b
children
comparison
equal deleted inserted replaced
19:15cd64d7c58b 20:f4d5237a84f6
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.10.1</token> 2 <token name="@TOOL_VERSION@">1.10.1</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@IDX_VERSION@">q7</token> 4 <token name="@IDX_VERSION@">q7</token>
5 <token name="@PROFILE_VERSION@">20.01</token> 5 <token name="@PROFILE_VERSION@">20.01</token>
6 <xml name="xrefs">
7 <xrefs>
8 <xref type="bio.tools">salmon</xref>
9 </xrefs>
10 </xml>
6 <xml name="requirements"> 11 <xml name="requirements">
7 <requirements> 12 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
9 <requirement type="package" version="1.3">seqtk</requirement> 14 <requirement type="package" version="1.3">seqtk</requirement>
10 <requirement type="package" version="1.16.1">samtools</requirement> 15 <requirement type="package" version="1.16.1">samtools</requirement>
119 <!--Salmon quant type select: reads-based or alignment-based--> 124 <!--Salmon quant type select: reads-based or alignment-based-->
120 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False" 125 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
121 label="Discard orphan quasi" 126 label="Discard orphan quasi"
122 help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/> 127 help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
123 <conditional name="validmap"> 128 <conditional name="validmap">
124 <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False" 129 <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.">
125 label="Validate mappings" 130 <option value="--validateMappings">True</option>
126 help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/> 131 <option value="" selected="true">False</option>
132 </param>
127 <when value="--validateMappings"> 133 <when value="--validateMappings">
128 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99" 134 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
129 label="Min Score Fraction" 135 label="Min Score Fraction"
130 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/> 136 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
131 <param name="maxMMPExtension" type="integer" optional="True" 137 <param name="maxMMPExtension" type="integer" optional="True"
388 #end if 394 #end if
389 #set $ext = 'fastq' 395 #set $ext = 'fastq'
390 #end if 396 #end if
391 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext && 397 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
392 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext && 398 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
393 #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved': 399 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
394 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta': 400 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
395 #set $ext = 'fasta' 401 #set $ext = 'fasta'
396 #else: 402 #else:
397 #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): 403 #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
398 #set compressed = 'GZ' 404 #set compressed = 'GZ'