Mercurial > repos > iuc > irma
diff irma.xml @ 1:736090e99c59 draft
planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402
| author | iuc |
|---|---|
| date | Wed, 22 Jan 2025 14:10:33 +0000 |
| parents | 3d86c05cd838 |
| children | 69ce61289a2a |
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--- a/irma.xml Sat Nov 09 13:53:38 2024 +0000 +++ b/irma.xml Wed Jan 22 14:10:33 2025 +0000 @@ -2,7 +2,7 @@ <description>Construct robust assemblies of highly variable RNA viruses</description> <macros> <token name="@TOOL_VERSION@">1.2.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">irma-virus</xref> @@ -126,8 +126,10 @@ <option value="FLU-pacbio">FLU-pacbio</option> </param> <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs"> + <option value="amended_consensus" selected="false">Amended consensus files: Include ambiguity codes for alleles, with second allele frequency greater 0.25</option> <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option> <option value="vcf" selected="false">Vcf: Variation calling file per segment</option> + <option value="run_info" selected="false">Run info: Text file with run metadata</option> </param> <conditional name="advanced_config"> <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file."> @@ -267,8 +269,8 @@ </inputs> <outputs> <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences"> + <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/> <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/> - <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/> <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/> <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/> <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/> @@ -277,10 +279,21 @@ <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/> </collection> <!-- optional outputs--> + <collection name="amended_collection" type="list" label="Amended Fasta Consensus"> + <filter>optional_outputs and 'amended_consensus' in optional_outputs</filter> + <data name="PB2" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_1.fa" label="PB2"/> + <data name="PB1" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_2.fa" label="PB1"/> + <data name="PA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_3.fa" label="PA"/> + <data name="HA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_4.fa" label="HA"/> + <data name="NP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_5.fa" label="NP"/> + <data name="NA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_6.fa" label="NA"/> + <data name="MP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_7.fa" label="MP"/> + <data name="NS" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_8.fa" label="NS"/> + </collection> <collection name="bam_collection" type="list" label="Alignment files (bam)"> <filter>optional_outputs and 'bam' in optional_outputs</filter> + <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/> <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/> - <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/> <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/> <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/> <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/> @@ -290,8 +303,8 @@ </collection> <collection name="vcf_collection" type="list" label="Variant calling files (VCF)"> <filter>optional_outputs and 'vcf' in optional_outputs</filter> + <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/> <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/> - <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/> <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/> <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/> <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/> @@ -299,6 +312,9 @@ <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/> <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/> </collection> + <data name="run_info" label="IRMA run info" format="txt" from_work_dir="resultDir/logs/run_info.txt"> + <filter>optional_outputs and 'run_info' in optional_outputs</filter> + </data> </outputs> <tests> <test expect_num_outputs="27"> @@ -454,6 +470,31 @@ <output_collection name="bam_collection" type="list" count="8" /> <output_collection name="vcf_collection" type="list" count="8" /> </test> + <test expect_num_outputs="19"> + <conditional name="input_type_conditional"> + <param name="fastq_input1" value="test_reads.fq" /> + <param name="input_type" value="single" /> + </conditional> + <conditional name="advanced_config"> + <param name="customize" value="no" /> + </conditional> + <param name="module" value="FLU-utr" /> + <param name="optional_outputs" value="amended_consensus,run_info"/> + <output_collection name="consensus_collection" type="list"> + <element name="HA"> + <assert_contents> + <has_n_lines n="2"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="amended_collection" type="list"> + <element name="HA"> + <assert_contents> + <has_n_lines n="2"/> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ .. class:: infomark