Mercurial > repos > iuc > metaphlan2
changeset 2:f60773e921fa draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit bfc25b2695b9689c60101f84162610194a33c886"
| author | iuc |
|---|---|
| date | Fri, 19 Mar 2021 21:39:32 +0000 |
| parents | 9be4beda6482 |
| children | |
| files | metaphlan2.xml test-data/input_sequences.fastq.gz |
| diffstat | 2 files changed, 27 insertions(+), 5 deletions(-) [+] |
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--- a/metaphlan2.xml Fri Mar 19 09:38:42 2021 +0000 +++ b/metaphlan2.xml Fri Mar 19 21:39:32 2021 +0000 @@ -34,7 +34,13 @@ #end if metaphlan2.py - '$input_file' + #if $input_file.datatype.file_ext.endswith(".gz") + <(zcat '$input_file') + #else if $input_file.datatype.file_ext.endswith(".bz2") + <(bzcat '$input_file') + #else + '$input_file' + #end if -o '$output_file' --input_type $ext --bowtie2_exe `which bowtie2` @@ -74,7 +80,7 @@ ]]></command> <inputs> - <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/> + <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2,sam" label="Input file"/> <conditional name="db"> <param name="db_selector" type="select" label="Database with clade-specific marker genes"> <option value="cached" selected="true">Locally cached</option> @@ -133,10 +139,10 @@ <tests> <test> - <param name="input_file" value="input_sequences.fasta"/> + <param name="input_file" value="input_sequences.fasta" ftype="fasta"/> <param name="db_selector" value="history" /> <param name="mpa_pkl" value="marker_metadata.json" /> - <param name="bowtie2db" value="marker_sequences.fasta" /> + <param name="bowtie2db" value="marker_sequences.fasta" ftype="fasta"/> <param name="analysis_type_select" value="rel_ab" /> <param name="taxonomic_level" value="a" /> <param name="min_cu_len" value="2000" /> @@ -146,7 +152,23 @@ <param name="ignore_bacteria" value="" /> <param name="ignore_archaea" value="" /> <param name="stat_q" value="0.1" /> - <output name="output_file" file="community_profile.tabular"/> + <output name="output_file" file="community_profile.tabular" ftype="tabular"/> + </test> + <test> + <param name="input_file" value="input_sequences.fastq.gz" ftype="fastqsanger.gz"/> + <param name="db_selector" value="history" /> + <param name="mpa_pkl" value="marker_metadata.json" /> + <param name="bowtie2db" value="marker_sequences.fasta" ftype="fasta"/> + <param name="analysis_type_select" value="rel_ab" /> + <param name="taxonomic_level" value="a" /> + <param name="min_cu_len" value="2000" /> + <param name="min_alignment_len" value="0" /> + <param name="ignore_viruses" value="" /> + <param name="ignore_eukaryotes" value="" /> + <param name="ignore_bacteria" value="" /> + <param name="ignore_archaea" value="" /> + <param name="stat_q" value="0.1" /> + <output name="output_file" file="community_profile.tabular" ftype="tabular"/> </test> </tests>