Mercurial > repos > iuc > stacks2_shortreads

comparison macros.xml @ 1:1974fee35ca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:16:13 -0400
parents ad7a60726fc3
children 43e3eeb2e0ec
comparison
equal deleted inserted replaced
0:ad7a60726fc3 1:1974fee35ca7
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 9
10 <token name="@STACKS_VERSION@">2.4</token> 10 <token name="@STACKS_VERSION@">2.4</token>
11 <token name="@WRAPPER_VERSION@">0</token> 11 <token name="@WRAPPER_VERSION@">1</token>
12 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 --> 12 <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
13 <token name="@PROFILE@">18.01</token> 13 <token name="@PROFILE@">18.01</token>
14 14
15 <xml name="citation"> 15 <xml name="citation">
16 <citations> 16 <citations>
214 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@"> 214 <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
215 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> 215 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
216 </expand> 216 </expand>
217 </xml> 217 </xml>
218 218
219 <!-- fastq input (used in denovomap, tsv2bam, ustacks) 219 <!-- fastq input (used in denovomap, tsv2bam, ustacks)
220 - fastq_optional: makes fastq input optional (true/false) 220 - fastq_optional: makes fastq input optional (true/false)
221 - se_option: wording for "single end" option (for tsv2bam this is the 221 - se_option: wording for "single end" option (for tsv2bam this is the
222 reverse reads for the others its the forward reads) 222 reverse reads for the others its the forward reads)
223 - help: help text --> 223 - help: help text -->
224 <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help=""> 224 <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
225 <conditional name="input_type"> 225 <conditional name="input_type">
566 <expand macro="snp_options"> 566 <expand macro="snp_options">
567 <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> 567 <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
568 </expand> 568 </expand>
569 </xml> 569 </xml>
570 570
571 <!-- variant calling option for use in gstacks and denovomap 571 <!-- variant calling option for use in gstacks and denovomap
572 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap) 572 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
573 otherwise no default is is available and gstacks will output and error 573 otherwise no default is is available and gstacks will output and error
574 "Error: No value was provided for \-\-var-alpha and there is no default for this model)" 574 "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
575 --> 575 -->
576 <xml name="variant_calling_options_vg" token_varalpha_default=""> 576 <xml name="variant_calling_options_vg" token_varalpha_default="">
577 <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." /> 577 <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
578 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" /> 578 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
579 </xml> 579 </xml>