Mercurial > repos > greg > vsnp_statistics

comparison vsnp_statistics.xml @ 5:d0fbdeaaa488 draft

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
author greg
date Wed, 16 Jun 2021 17:38:47 +0000
parents 2d6c6b01319e
children de2af65c4633
comparison
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4:2d6c6b01319e 5:d0fbdeaaa488
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.78">biopython</requirement>
7 <requirement type="package" version="1.16.5">numpy</requirement> 8 <requirement type="package" version="1.16.5">numpy</requirement>
8 <requirement type="package" version="0.25.3">pandas</requirement> 9 <requirement type="package" version="0.25.3">pandas</requirement>
9 <requirement type="package" version="1.2.0">xlrd</requirement> 10 <requirement type="package" version="1.2.0">xlrd</requirement>
10 <requirement type="package" version="1.2.8">xlsxwriter</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #import re 13 #import re
14 #set input_idxstats_dir = 'input_idxstats' 14 #set input_idxstats_dir = 'input_idxstats'
15 #set input_metrics_dir = 'input_metrics' 15 #set input_metrics_dir = 'input_metrics'
119 <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/> 119 <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/>
120 </when> 120 </when>
121 </conditional> 121 </conditional>
122 </inputs> 122 </inputs>
123 <outputs> 123 <outputs>
124 <data name="output" format="xlsx"/> 124 <data name="output" format="tabular"/>
125 </outputs> 125 </outputs>
126 <tests> 126 <tests>
127 <!-- A single fastq file --> 127 <!-- A single fastq file -->
128 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
129 <param name="input_type" value="single_files"/> 129 <param name="input_type" value="single_files"/>
130 <param name="read_type" value="single"/> 130 <param name="read_type" value="single"/>
131 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> 131 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
132 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> 132 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/>
133 <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> 133 <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/>
134 <output name="output" file="vsnp_statistics1.xlsx" ftype="xlsx" compare="sim_size"/> 134 <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/>
135 </test> 135 </test>
136 <!-- A set of paired fastq files --> 136 <!-- A set of paired fastq files -->
137 <test expect_num_outputs="1"> 137 <test expect_num_outputs="1">
138 <param name="input_type" value="single_files"/> 138 <param name="input_type" value="single_files"/>
139 <param name="read_type" value="pair"/> 139 <param name="read_type" value="pair"/>
140 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> 140 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
141 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> 141 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
142 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> 142 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/>
143 <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> 143 <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/>
144 <output name="output" file="vsnp_statistics2.xlsx" ftype="xlsx" compare="sim_size"/> 144 <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/>
145 </test> 145 </test>
146 <!-- A collection of SE fastq files --> 146 <!-- A collection of SE fastq files -->
147 <test expect_num_outputs="1"> 147 <test expect_num_outputs="1">
148 <param name="input_type" value="collections"/> 148 <param name="input_type" value="collections"/>
149 <param name="read_type" value="single"/> 149 <param name="read_type" value="single"/>
163 <collection type="list"> 163 <collection type="list">
164 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/> 164 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/>
165 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/> 165 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/>
166 </collection> 166 </collection>
167 </param> 167 </param>
168 <output name="output" file="vsnp_statistics3.xlsx" ftype="xlsx" compare="sim_size"/> 168 <output name="output" file="vsnp_statistics3.tabular" ftype="tabular"/>
169 </test> 169 </test>
170 <!-- A collection of PE fastq files --> 170 <!-- A collection of PE fastq files -->
171 <test expect_num_outputs="1"> 171 <test expect_num_outputs="1">
172 <param name="input_type" value="collections"/> 172 <param name="input_type" value="collections"/>
173 <param name="collection_type" value="paired"/> 173 <param name="collection_type" value="paired"/>
185 <param name="vsnp_azc"> 185 <param name="vsnp_azc">
186 <collection type="list"> 186 <collection type="list">
187 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/> 187 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/>
188 </collection> 188 </collection>
189 </param> 189 </param>
190 <output name="output" file="vsnp_statistics4.xlsx" ftype="xlsx" compare="sim_size"/> 190 <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/>
191 </test> 191 </test>
192 </tests> 192 </tests>
193 <help> 193 <help>
194 **What it does** 194 **What it does**
195 195