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comparison stacks_gstacks.xml @ 4:7370bb65bad4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:29:04 +0000
parents eb784fa07f80
children f6e91108b7b1
comparison
equal deleted inserted replaced
3:eb784fa07f80 4:7370bb65bad4
2 <description>Call variants, genotypes and haplotype</description> 2 <description>Call variants, genotypes and haplotype</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.9">samtools</requirement> 7 <requirement type="package" version="1.13">samtools</requirement>
8 </expand> 8 </expand>
9 <expand macro="version_cmd"/> 9 <expand macro="version_cmd"/>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @FASTQ_INPUT_FUNCTIONS@ 11 @FASTQ_INPUT_FUNCTIONS@
12 12
86 ## (https://groups.google.com/d/msg/stacks-users/CazwJY1DPGA/7vuahiB2GgAJ) 86 ## (https://groups.google.com/d/msg/stacks-users/CazwJY1DPGA/7vuahiB2GgAJ)
87 ## so we fix them temporarily by piping them through samtools view (disabling all 87 ## so we fix them temporarily by piping them through samtools view (disabling all
88 ## exit codes and stderr output) this adds the samtools requirement 88 ## exit codes and stderr output) this adds the samtools requirement
89 ## for later versions where this is fixed the output bam files could just be moved 89 ## for later versions where this is fixed the output bam files could just be moved
90 ## to stacks_outputs if this is still necessary 90 ## to stacks_outputs if this is still necessary
91 #if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != "" 91 #if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments
92 #if $popmap: 92 #if $popmap:
93 && for b in stacks_outputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done 93 && for b in stacks_outputs/*alns.bam; do (samtools view --no-PG -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
94 #else 94 #else
95 && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam 95 && (samtools view --no-PG -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
96 #end if 96 #end if
97 #end if 97 #end if
98 98
99 @EXTRACT_VCF@ 99 @EXTRACT_VCF@
100 100
115 <param name="mode_select" type="select" label="Mode"> 115 <param name="mode_select" type="select" label="Mode">
116 <option value="denovo" selected="true">De novo mode</option> 116 <option value="denovo" selected="true">De novo mode</option>
117 <option value="refbased">Reference-based</option> 117 <option value="refbased">Reference-based</option>
118 </param> 118 </param>
119 <when value="denovo"> 119 <when value="denovo">
120 <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/> 120 <param argument="--ignore-pe-reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
121 <conditional name="advanced_cond"> 121 <conditional name="advanced_cond">
122 <param name="advanced_select" type="select" label="Advanced options"> 122 <param name="advanced_select" type="select" label="Advanced options">
123 <option value="no">No</option> 123 <option value="no">No</option>
124 <option value="yes">Yes</option> 124 <option value="yes">Yes</option>
125 </param> 125 </param>
126 <when value="yes"> 126 <when value="yes">
127 <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/> 127 <param argument="--kmer-length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
128 <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/> 128 <param argument="--max-debruijn-reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
129 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/> 129 <param argument="--min-kmer-cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
130 <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/> 130 <param argument="--write-alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
131 </when> 131 </when>
132 <when value="no"/> 132 <when value="no"/>
133 </conditional> 133 </conditional>
134 </when> 134 </when>
135 <when value="refbased"> 135 <when value="refbased">
138 <option value="" selected="true">single/paired</option> 138 <option value="" selected="true">single/paired</option>
139 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> 139 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
140 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option> 140 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
141 </param> 141 </param>
142 <when value=""> 142 <when value="">
143 <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/> 143 <param argument="--rm-unpaired-reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
144 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/> 144 <param argument="--rm-pcr-duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
145 </when> 145 </when>
146 <when value="--unpaired"/> 146 <when value="--unpaired"/>
147 <when value="--ignore-pe-reads"/> 147 <when value="--ignore-pe-reads"/>
148 </conditional> 148 </conditional>
149 <conditional name="advanced_cond"> 149 <conditional name="advanced_cond">
150 <param name="advanced_select" type="select" label="Advanced options"> 150 <param name="advanced_select" type="select" label="Advanced options">
151 <option value="no">No</option> 151 <option value="no">No</option>
152 <option value="yes">Yes</option> 152 <option value="yes">Yes</option>
153 </param> 153 </param>
154 <when value="yes"> 154 <when value="yes">
155 <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/> 155 <param argument="--min-mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
156 <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/> 156 <param argument="--max-clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
157 <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/> 157 <param argument="--max-insert-len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
158 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/> 158 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/>
159 <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/> 159 <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/>
160 <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/> 160 <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>
161 <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/> 161 <param argument="--phasing-dont-prune-hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
162 </when> 162 </when>
163 <when value="no"/> 163 <when value="no"/>
164 </conditional> 164 </conditional>
165 </when> 165 </when>
166 </conditional> 166 </conditional>
201 <param name="add_log_distribs" value="yes"/> 201 <param name="add_log_distribs" value="yes"/>
202 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/> 202 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
203 <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/> 203 <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/>
204 <output_collection name="gstacks_out" type="list" count="2"> 204 <output_collection name="gstacks_out" type="list" count="2">
205 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/> 205 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
206 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/> 206 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" decompress="true" compare="diff"/>
207 </output_collection> 207 </output_collection>
208 </test> 208 </test>
209 <!-- denovomode, w popmap, write alignments --> 209 <!-- denovomode, w popmap, write alignments -->
210 <test expect_num_outputs="3"> 210 <test expect_num_outputs="3">
211 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/> 211 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
212 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> 212 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
213 <conditional name="mode_cond"> 213 <conditional name="mode_cond">
214 <param name="mode_select" value="denovo"/> 214 <param name="mode_select" value="denovo"/>
215 <conditional name="advanced_cond"> 215 <conditional name="advanced_cond">
216 <param name="advanced_select" value="yes"/> 216 <param name="advanced_select" value="yes"/>
217 <param name="write_alignments" value="--write-alignments"/> 217 <param name="write_alignments" value="true"/>
218 </conditional> 218 </conditional>
219 </conditional> 219 </conditional>
220 <param name="add_log" value="yes"/> 220 <param name="add_log" value="yes"/>
221 <assert_command> 221 <assert_command>
222 <has_text text="--write-alignments"/> 222 <has_text text="--write-alignments"/>