Mercurial > repos > iuc > metaphlan
diff metaphlan.xml @ 13:ef65b083bd0c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
| author | iuc |
|---|---|
| date | Sun, 08 Sep 2024 06:59:00 +0000 |
| parents | 1a037928504c |
| children |
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--- a/metaphlan.xml Sun Aug 11 20:35:53 2024 +0000 +++ b/metaphlan.xml Sun Sep 08 06:59:00 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>to profile the composition of microbial communities</description> <macros> <import>macros.xml</import> @@ -26,7 +26,7 @@ <when value="s"/> </conditional> </xml> - <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token> + <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz</token> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> @@ -74,13 +74,19 @@ #if $full_ext.endswith("gz") zcat '$inputs.in.raw_in.in_f' > 'in_f' && zcat '$inputs.in.raw_in.in_r' > 'in_r' && - #set file_path="-1 in_f -2 in_r" #else if $full_ext.endswith("bz2") bzcat '$inputs.in.raw_in.in_f' > 'in_f' && bzcat '$inputs.in.raw_in.in_r' > 'in_r' && #set file_path="-1 in_f -2 in_r" + ln -s '$inputs.in.raw_in.in_f' 'in_f' && + ln -s '$inputs.in.raw_in.in_r' 'in_r' && + #end if + ## paired data has by default no special treatment, i.e. it is given as comma separated list + ## except iff paired subsampling where -1 and -2 must be used + #if $subsample.selector == 'paired' + #set file_path="-1 in_f -2 in_r" #else - #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r) + #set file_path="in_f,in_r" #end if #else if $inputs.in.raw_in.selector == "paired_collection" #set full_ext=$inputs.in.raw_in.in.forward.ext @@ -91,13 +97,17 @@ #if $full_ext.endswith("gz") zcat '$inputs.in.raw_in.in.forward' > 'in_f' && zcat '$inputs.in.raw_in.in.reverse' > 'in_r' && - #set file_path="-1 in_f -2 in_r" #else if $full_ext.endswith("bz2") bzcat '$inputs.in.raw_in.in.forward' > 'in_f' && bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' && + #else + ln -s '$inputs.in.raw_in.in.forward' 'in_f' && + ln -s '$inputs.in.raw_in.in.reverse' 'in_r' && + #end if + #if $subsample.selector == 'paired' #set file_path="-1 in_f -2 in_r" #else - #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r) + #set file_path="in_f,in_r" #end if #end if @@ -983,6 +993,87 @@ <has_text text="Downloading" negate="true"/> </assert_stderr> </test> + <!-- Paired fastq file as collection, Cached db --> + <test expect_num_outputs="4"> + <section name="inputs"> + <conditional name="in"> + <param name="selector" value="raw"/> + <conditional name="raw_in"> + <param name="selector" value="paired_collection"/> + <param name="in"> + <collection type="paired" name="pair"> + <element name="forward" value="SRS014464-Anterior_nares_mini.fastq" /> + <element name="reverse" value="SRS014464-Anterior_nares_mini.fastq" /> + </collection> + </param> + </conditional> + <param name="read_min_len" value="70"/> + <section name="mapping"> + <param name="bt2_ps" value="sensitive"/> + <param name="min_mapq_val" value="5"/> + </section> + </conditional> + <conditional name="db"> + <param name="db_selector" value="cached"/> + <param name="cached_db" value="test-db-20210409"/> + </conditional> + </section> + <section name="analysis"> + <conditional name="analysis_type"> + <param name="t" value="rel_ab"/> + <conditional name="tax_lev"> + <param name="tax_lev" value="a"/> + <param name="split_levels" value="false"/> + </conditional> + </conditional> + <param name="min_cu_len" value="2000"/> + <param name="organism_profiling" value="add_viruses"/> + <param name="stat" value="avg_g"/> + <param name="stat_q" value="0.2"/> + <param name="perc_nonzero" value="0.33"/> + <param name="avoid_disqm" value="true"/> + </section> + <conditional name="subsample"> + <param name="selector" value="no"/> + </conditional> + <section name="out"> + <param name="sample_id_key" value="SampleID"/> + <param name="sample_id" value="Metaphlan_Analysis"/> + <param name="use_group_representative" value="false"/> + <param name="legacy_output" value="false"/> + <param name="CAMI_format_output" value="false"/> + <param name="unclassified_estimation" value="false"/> + <param name="krona_output" value="false"/> + </section> + <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> + <assert_contents> + <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> + <has_text text="relative_abundance"/> + <has_text text="NCBI_tax_id"/> + <has_text text="clade_name"/> + </assert_contents> + </output> + <output name="bowtie2out" ftype="tabular"> + <assert_contents> + <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/> + <has_text text="90240__A0A378QWM4__NCTC12877_00123"/> + </assert_contents> + </output> + <output name="sam_output_file" ftype="sam"> + <assert_contents> + <has_size min="8450" max="8550"/> + <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> + </assert_contents> + </output> + <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size"> + <assert_contents> + <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> + </assert_contents> + </output> + <assert_stderr> + <has_text text="Downloading" negate="true"/> + </assert_stderr> + </test> <!-- SAM, cached DB --> <test expect_num_outputs="2"> <section name="inputs">