Mercurial > repos > matthias > stacks2_cstacks

comparison macros.xml @ 5:687f84474d33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:12:36 -0400
parents 924e7889aa05
children c8f5a29f720c
comparison
equal deleted inserted replaced
4:924e7889aa05 5:687f84474d33
5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> 5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 9
10 <token name="@STACKS_VERSION@">2.3c</token> 10 <token name="@STACKS_VERSION@">2.4</token>
11 <token name="@WRAPPER_VERSION@">0</token> 11 <token name="@WRAPPER_VERSION@">0</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">
114 #if $output_log 114 #if $output_log
115 cat $output_log 2>&1 115 cat $output_log 2>&1
116 #end if 116 #end if
117 ]]></token> 117 ]]></token>
118 <xml name="in_log"> 118 <xml name="in_log">
119 <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> 119 <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
120 </xml> 120 </xml>
121 <xml name="out_log"> 121 <xml name="out_log">
122 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> 122 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
123 <filter>add_log</filter> 123 <filter>add_log</filter>
124 </data> 124 </data>
136 </xml> 136 </xml>
137 <xml name="bam_input_macro"> 137 <xml name="bam_input_macro">
138 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" /> 138 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />
139 </xml> 139 </xml>
140 <xml name="input_aln_macro"> 140 <xml name="input_aln_macro">
141 <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> 141 <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
142 </xml> 142 </xml>
143 143
144 <!-- code for creating links to the data sets from previous pipeline steps 144 <!-- code for creating links to the data sets from previous pipeline steps
145 - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv) 145 - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv)
146 also stores sample names in list (samples) 146 also stores sample names in list (samples)
210 <yield/> 210 <yield/>
211 </xml> 211 </xml>
212 212
213 <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired"> 213 <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
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 <xml name="fastq_input" token_fastq_optional="false" token_help=""> 220 <xml name="fastq_input" token_fastq_optional="false" token_help="">
507 </data> 507 </data>
508 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped"> 508 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped">
509 <filter>populations_output['plink']</filter> 509 <filter>populations_output['plink']</filter>
510 </data> 510 </data>
511 511
512 <!--structure populations.hzar-->
513 <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv">
514 <filter>populations_output['hzar']</filter>
515 </data>
512 <!--structure populations.structure--> 516 <!--structure populations.structure-->
513 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> 517 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
514 <filter>populations_output['structure']</filter> 518 <filter>populations_output['structure']</filter>
515 </data> 519 </data>
516 520
558 <expand macro="snp_options"> 562 <expand macro="snp_options">
559 <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"/> 563 <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"/>
560 </expand> 564 </expand>
561 </xml> 565 </xml>
562 566
563 <!-- variant calling option for use in gstacks and denovomap --> 567 <!-- variant calling option for use in gstacks and denovomap
564 <xml name="variant_calling_options_vg"> 568 default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
565 <param argument="--var-alpha" name="var_alpha" type="float" value="0.01" min="0" label="Alpha threshold for discovering SNPs" /> 569 otherwise no default is is available and gstacks will output and error
570 "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
571 -->
572 <xml name="variant_calling_options_vg" token_varalpha_default="">
573 <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." />
566 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" /> 574 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
567 </xml> 575 </xml>
568 576
569 <xml name="barcode_encoding_single" token_type=""> 577 <xml name="barcode_encoding_single" token_type="">
570 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> 578 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>