Mercurial > repos > devteam > fastq_paired_end_interlacer
comparison fastq_paired_end_interlacer.xml @ 5:15fab8bda4e3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
| author | iuc |
|---|---|
| date | Fri, 04 Oct 2024 10:33:39 +0000 |
| parents | 49b7bc41c7b0 |
| children |
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| 4:49b7bc41c7b0 | 5:15fab8bda4e3 |
|---|---|
| 1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1+galaxy0"> | 1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>on paired end reads</description> | 2 <description>on paired end reads</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 3 <edam_topics> | 6 <edam_topics> |
| 4 <edam_topic>topic_0622</edam_topic> | 7 <edam_topic>topic_0622</edam_topic> |
| 5 </edam_topics> | 8 </edam_topics> |
| 6 <edam_operations> | 9 <edam_operations> |
| 7 <edam_operation>operation_3436</edam_operation> | 10 <edam_operation>operation_3436</edam_operation> |
| 8 </edam_operations> | 11 </edam_operations> |
| 9 <macros> | |
| 10 <import>macros.xml</import> | |
| 11 </macros> | |
| 12 <expand macro="requirements"/> | 12 <expand macro="requirements"/> |
| 13 <command><![CDATA[ | 13 <command><![CDATA[ |
| 14 gx-fastq-paired-end-interlacer | 14 gx-fastq-paired-end-interlacer |
| 15 #if $reads.reads_selector == 'paired' | 15 #if $reads.reads_selector == 'paired' |
| 16 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} | 16 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} |
| 51 <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}"> | 51 <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}"> |
| 52 <filter>reads['reads_selector'] == 'paired_collection'</filter> | 52 <filter>reads['reads_selector'] == 'paired_collection'</filter> |
| 53 </data> | 53 </data> |
| 54 </outputs> | 54 </outputs> |
| 55 <tests> | 55 <tests> |
| 56 <test> | 56 <test expect_num_outputs="2"> |
| 57 <param name="reads_selector" value="paired" /> | 57 <param name="reads_selector" value="paired" /> |
| 58 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> | 58 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
| 59 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> | 59 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |
| 60 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> | 60 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> |
| 61 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> | 61 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> |
| 62 </test> | 62 </test> |
| 63 <test> | 63 <test expect_num_outputs="2"> |
| 64 <param name="reads_selector" value="paired" /> | 64 <param name="reads_selector" value="paired" /> |
| 65 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> | 65 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> |
| 66 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> | 66 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> |
| 67 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> | 67 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> |
| 68 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> | 68 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> |
| 69 </test> | 69 </test> |
| 70 <test> | 70 <test expect_num_outputs="2"> |
| 71 <param name="reads_selector" value="paired" /> | 71 <param name="reads_selector" value="paired" /> |
| 72 <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> | 72 <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> |
| 73 <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> | 73 <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> |
| 74 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> | 74 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> |
| 75 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> | 75 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> |
| 76 </test> | 76 </test> |
| 77 <test> | 77 <test expect_num_outputs="2"> |
| 78 <param name="reads_selector" value="paired" /> | 78 <param name="reads_selector" value="paired" /> |
| 79 <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> | 79 <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> |
| 80 <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> | 80 <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> |
| 81 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> | 81 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> |
| 82 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> | 82 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> |
| 83 </test> | 83 </test> |
| 84 <test> | 84 <test expect_num_outputs="2"> |
| 85 <param name="reads_selector" value="paired_collection" /> | 85 <param name="reads_selector" value="paired_collection" /> |
| 86 <param name="reads_coll"> | 86 <param name="reads_coll"> |
| 87 <collection type="paired"> | 87 <collection type="paired"> |
| 88 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> | 88 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
| 89 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> | 89 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |