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comparison fastq_groupmerge.xml @ 1:bbc3d29a94e5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
author iuc
date Thu, 13 Nov 2025 15:33:46 +0000
parents acdbb0af0a75
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0:acdbb0af0a75 1:bbc3d29a94e5
1 <tool id="fastq_groupmerge" name="Fastq groupmerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="fastq_groupmerge" name="Fastq groupmerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Group FASTQ files together based on a set grouping in a metadata file</description>
2 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">1.0.1</token> 4 <token name="@TOOL_VERSION@">1.0.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">25.0</token> 6 <token name="@PROFILE@">25.0</token>
6 </macros> 7 </macros>
7 <requirements> 8 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">fastq-groupmerge</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">fastq-groupmerge</requirement>
49 <param name="is_select" type="select" label="Check type of fastq read library"> 50 <param name="is_select" type="select" label="Check type of fastq read library">
50 <option value="single">Single reads</option> 51 <option value="single">Single reads</option>
51 <option value="pair" selected="true">Paired reads</option> 52 <option value="pair" selected="true">Paired reads</option>
52 </param> 53 </param>
53 <when value="single"> 54 <when value="single">
54 <param name="samples" type="data_collection" collection_type="list" format="fastq,fastq.gz" label="Input single sample(s) read(s)"/> 55 <param name="samples" type="data_collection" collection_type="list" format="fastqsanger,fastqsanger.gz" label="Input single sample(s) read(s)"/>
55 </when> 56 </when>
56 <when value="pair"> 57 <when value="pair">
57 <param name="samples" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="Input paired sample(s) read(s) collection"/> 58 <param name="samples" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Input paired sample(s) read(s) collection"/>
58 </when> 59 </when>
59 </conditional> 60 </conditional>
60 <param argument="--metadata" type="data" multiple="false" format="tabular,csv,tsv" optional="true" label="Metadata table file" help="Metadata file with first column sample name and another column with group ID. Multiple grouping is allowed, see the help section. If no metadata table is provided, this tool will merge all samples!"/> 61 <param argument="--metadata" type="data" multiple="false" format="tabular,csv,tsv" optional="true" label="Metadata table file" help="Metadata file with first column sample name and another column with group ID. Multiple grouping is allowed, see the help section. If no metadata table is provided, this tool will merge all samples!"/>
61 <param argument="--group_col" type="text" value="group" label="Input the column name of the `group` column" help="The metadata file should contain two columns, one with the sample names and one with sample group ID. Use the same ID for samples that should be grouped. Look at the help section for more information!"/> 62 <param argument="--group_col" type="text" value="group" label="Input the column name of the `group` column" help="The metadata file should contain two columns, one with the sample names and one with sample group ID. Use the same ID for samples that should be grouped. Look at the help section for more information!"/>
62 </inputs> 63 </inputs>
82 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/> 83 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
83 </collection> 84 </collection>
84 </element> 85 </element>
85 <element name="B1"> 86 <element name="B1">
86 <collection type="paired"> 87 <collection type="paired">
87 <element name="forward" value="B1_forward.fastq" ftype="fastq"/> 88 <element name="forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
88 <element name="reverse" value="B1_reverse.fastq" ftype="fastq"/> 89 <element name="reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
89 </collection> 90 </collection>
90 </element> 91 </element>
91 </collection> 92 </collection>
92 </param> 93 </param>
93 </conditional> 94 </conditional>
137 <param name="is_select" value="single"/> 138 <param name="is_select" value="single"/>
138 <param name="samples"> 139 <param name="samples">
139 <collection type="list"> 140 <collection type="list">
140 <element name="A1_forward" value="A1_forward.fastq.gz" ftype="fastq.gz"/> 141 <element name="A1_forward" value="A1_forward.fastq.gz" ftype="fastq.gz"/>
141 <element name="A1_reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/> 142 <element name="A1_reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
142 <element name="B1_forward" value="B1_forward.fastq" ftype="fastq"/> 143 <element name="B1_forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
143 <element name="B1_reverse" value="B1_reverse.fastq" ftype="fastq"/> 144 <element name="B1_reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
144 </collection> 145 </collection>
145 </param> 146 </param>
146 </conditional> 147 </conditional>
147 <param name="metadata" value="metadata_single.csv" ftype="csv"/> 148 <param name="metadata" value="metadata_single.csv" ftype="csv"/>
148 <output_collection name="merged_samples_single" type="list" count="1"> 149 <output_collection name="merged_samples_single" type="list" count="1">
160 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/> 161 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
161 </collection> 162 </collection>
162 </element> 163 </element>
163 <element name="B1"> 164 <element name="B1">
164 <collection type="paired"> 165 <collection type="paired">
165 <element name="forward" value="B1_forward.fastq" ftype="fastq"/> 166 <element name="forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
166 <element name="reverse" value="B1_reverse.fastq" ftype="fastq"/> 167 <element name="reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
167 </collection> 168 </collection>
168 </element> 169 </element>
169 </collection> 170 </collection>
170 </param> 171 </param>
171 </conditional> 172 </conditional>