Mercurial > repos > iuc > fastq_groupmerge

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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
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acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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1 <tool id="fastq_groupmerge" name="Fastq groupmerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
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2 <description>Group FASTQ files together based on a set grouping in a metadata file</description>
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acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">25.0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">fastq-groupmerge</requirement>
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10 </requirements>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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11 <command detect_errors="exit_code">
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12 <![CDATA[
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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14 mkdir 'output' 'samples' &&
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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16 #if $input.is_select == "pair":
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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17 #for $sample in $samples:
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18 ln -s '$sample.forward' 'samples/${sample.element_identifier}_forward.${sample.forward.ext}' &&
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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19 ln -s '$sample.reverse' 'samples/${sample.element_identifier}_reverse.${sample.reverse.ext}' &&
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20 #end for
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21 #else:
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22 #for $sample in $samples:
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23 ln -s '$sample' 'samples/$sample.element_identifier.${sample.ext}' &&
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24 #end for
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25 #end if
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26
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27 fastq_groupmerge.py
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28 'samples'
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29 'output'
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30 #if $metadata:
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31 --metadata '$metadata'
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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32 --group_col '$group_col'
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33 #if $metadata.ext == "csv"
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34 --sep ","
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35 #else
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36 --sep "\t"
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37 #end if
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38 #end if
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39 #if $input.is_select == 'pair':
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40 --forward_suffix '_forward'
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41 --reverse_suffix '_reverse'
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42 #else:
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43 --single_reads
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44 #end if
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45
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46 ]]>
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47 </command>
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48 <inputs>
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49 <conditional name="input">
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50 <param name="is_select" type="select" label="Check type of fastq read library">
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51 <option value="single">Single reads</option>
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52 <option value="pair" selected="true">Paired reads</option>
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53 </param>
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54 <when value="single">
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55 <param name="samples" type="data_collection" collection_type="list" format="fastqsanger,fastqsanger.gz" label="Input single sample(s) read(s)"/>
0
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56 </when>
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57 <when value="pair">
1
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58 <param name="samples" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Input paired sample(s) read(s) collection"/>
0
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59 </when>
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60 </conditional>
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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!"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
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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!"/>
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63 </inputs>
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64 <outputs>
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65 <collection name="merged_samples_pairs" type="list:paired" label="${tool.name} on ${on_string}: Merged samples (pairs)">
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66 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq.gz" ext="fastq.gz" directory="output"/>
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67 <filter>input['is_select'] == 'pair'</filter>
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68 </collection>
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69 <collection name="merged_samples_single" type="list" label="${tool.name} on ${on_string}: Merged samples (single)">
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70 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)\.fastq.gz" ext="fastq.gz" directory="output"/>
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71 <filter>input['is_select'] == 'single'</filter>
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72 </collection>
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73 </outputs>
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74 <tests>
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75 <test expect_num_outputs="1">
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76 <conditional name="input">
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77 <param name="is_select" value="pair"/>
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78 <param name="samples">
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79 <collection type="list:paired">
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80 <element name="A1">
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81 <collection type="paired">
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82 <element name="forward" value="A1_forward.fastq.gz" ftype="fastq.gz"/>
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83 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
84 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
85 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
86 <element name="B1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
87 <collection type="paired">
1
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
88 <element name="forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
89 <element name="reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
90 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
91 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
92 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
93 </param>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
94 </conditional>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
95 <param name="metadata" value="metadata_1.csv" ftype="tabular"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
96 <param name="group_col" value="TEST_COLUMN"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
97 <output_collection name="merged_samples_pairs" type="list:paired" count="2">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
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diff changeset
98 <element name="control">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
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diff changeset
99 <element name="forward" value="control_forward.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
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diff changeset
100 <element name="reverse" value="control_reverse.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
101 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
102 <element name="single">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
103 <element name="forward" value="single_forward.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
104 <element name="reverse" value="single_reverse.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
105 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
106 </output_collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
107 </test>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
108 <test expect_num_outputs="1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
109 <conditional name="input">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
110 <param name="is_select" value="pair"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
111 <param name="samples">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
112 <collection type="list:paired">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
113 <element name="A2">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
114 <collection type="paired">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
115 <element name="forward" value="A2_R1.fastq" ftype="fastq"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
116 <element name="reverse" value="A2_R2.fastq" ftype="fastq"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
117 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
118 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
119 <element name="B2">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
120 <collection type="paired">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
121 <element name="forward" value="B2_R1.fastq" ftype="fastq"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
122 <element name="reverse" value="B2_R2.fastq" ftype="fastq"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
123 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
124 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
125 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
126 </param>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
127 </conditional>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
128 <param name="metadata" value="metadata_2.csv" ftype="csv"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
129 <output_collection name="merged_samples_pairs" type="list:paired" count="1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
130 <element name="treatment">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
131 <element name="forward" value="treatment_forward.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
132 <element name="reverse" value="treatment_reverse.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
133 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
134 </output_collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
135 </test>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
136 <test expect_num_outputs="1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
137 <conditional name="input">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
138 <param name="is_select" value="single"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
139 <param name="samples">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
140 <collection type="list">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
141 <element name="A1_forward" value="A1_forward.fastq.gz" ftype="fastq.gz"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
142 <element name="A1_reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
1
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
143 <element name="B1_forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
144 <element name="B1_reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
145 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
146 </param>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
147 </conditional>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
148 <param name="metadata" value="metadata_single.csv" ftype="csv"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
149 <output_collection name="merged_samples_single" type="list" count="1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
150 <element name="Test" value="Test.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
151 </output_collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
152 </test>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
153 <test expect_num_outputs="1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
154 <conditional name="input">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
155 <param name="is_select" value="pair"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
156 <param name="samples">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
157 <collection type="list:paired">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
158 <element name="A1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
159 <collection type="paired">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
160 <element name="forward" value="A1_forward.fastq.gz" ftype="fastq.gz"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
161 <element name="reverse" value="A1_reverse.fastq.gz" ftype="fastq.gz"/>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
162 </collection>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
163 </element>
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
164 <element name="B1">
acdbb0af0a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 0fbad98c785e4baf5a82b880ff1c5e2d19a81431
iuc
parents:
diff changeset
165 <collection type="paired">
1
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
166 <element name="forward" value="B1_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
bbc3d29a94e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge commit 19ea498c50afa7509379116596bc6d5287a6ba2b
iuc
parents: 0
diff changeset
167 <element name="reverse" value="B1_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
0
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168 </collection>
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169 </element>
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170 </collection>
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171 </param>
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172 </conditional>
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173 <output_collection name="merged_samples_pairs" type="list:paired" count="1">
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174 <element name="merged">
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175 <element name="forward" value="merged_forward.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
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176 <element name="reverse" value="merged_reverse.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
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177 </element>
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178 </output_collection>
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179 </test>
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180 </tests>
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181 <help>
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182 <![CDATA[
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183
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184 **What does this tool**
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185
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186 This tool is designed to group sample fastq reads together based on a grouping defined in a metadata file.
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187 This tool can be used to support grouped-assembly. In some cases you want to group them in multiple ways. E.g. merge technical replicas but also merge samples from similar samples (e.g. all from the gut). To this end you can provide multiple groupings.
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188
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189 **Input**
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190
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191 - A collection of pair reads which can be in fastq or fastq format
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192 - OPTIONAL BUT RECOMMENDED: a metadata file either tab separated in format: tabular/tsv or comma-separated in format: csv
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193
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194 The metadata file can look look like this for example:
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195
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196 .. metadata table::
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197
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198 sample_id,group
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199 A1,control
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200 B1,control
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201 A1,A1
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202 Test,
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203 ,Test
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204
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205 Important to this:
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206
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207 - The metadata file required to have a column sample_id with sample names (this are the pair name for example 'A1' is the pair collection name so 'A1' has to be written in the sample_id column) when using the pair collection option.
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208 - The column 'group' can be called anything. All samples with the same ID will be merged together in the output file. In the example file the output 'control_forward.fastq.gz' will contain the forward reads from 'A1' and 'B1'
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209 - When there is a empty entry in any column this line will be ignored!
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210 - When using the single read option note that in the 'sample_id' column the file name has to be stated completely therefore as example for input 'test_read.fastq' a line in the metadata table has to be 'test_read'
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211 - If metadata file is given only the sample reads stated in this file will be taken into account so you can also add the collection where other sample reads in this collection, they will be ignored if there are not stated in the metadata file!
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212
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213 **Output**
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214
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215 - For each group stated in the 'group' column a forward file [{group_name}_{forward_suffix}.fastq.gz] and a reverse file [{group_name}_{reverse_suffix}.fastq.gz] will be created
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216 - When no metadata is given all inputs which match to the 'forward_suffix' and 'reverse_suffix' will be merged together into one file each for forward and reverse!
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217
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218 ]]>
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219 </help>
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220 <citations>
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221 <citation type="bibtex">@misc{BibEntry2025Oct,
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222 title = {{fastq-groupmerge}},
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223 author = {Santino Faack (SantaMcCloud)},
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224 journal = {GitHub},
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225 year = {2025},
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226 month = oct,
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227 url = {https://github.com/SantaMcCloud/fastq-groupmerge}
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228 }</citation>
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229 </citations>
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230 </tool>