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comparison metaphlan.xml @ 9:f0ca613c512a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
author iuc
date Sun, 08 Sep 2024 06:57:40 +0000
parents 1416b7c401a3
children 392430381492
comparison
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8:1416b7c401a3 9:f0ca613c512a
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>to profile the composition of microbial communities</description> 2 <description>to profile the composition of microbial communities</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="tax_lev"> 5 <xml name="tax_lev">
6 <conditional name="tax_lev"> 6 <conditional name="tax_lev">
24 <when value="f"/> 24 <when value="f"/>
25 <when value="g"/> 25 <when value="g"/>
26 <when value="s"/> 26 <when value="s"/>
27 </conditional> 27 </conditional>
28 </xml> 28 </xml>
29 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token> 29 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz</token>
30 </macros> 30 </macros>
31 <expand macro="edam_ontology"/> 31 <expand macro="edam_ontology"/>
32 <expand macro="requirements"/> 32 <expand macro="requirements"/>
33 <version_command>metaphlan -v</version_command> 33 <version_command>metaphlan -v</version_command>
34 <command detect_errors="aggressive"><![CDATA[ 34 <command detect_errors="aggressive"><![CDATA[
72 exit 1 72 exit 1
73 #end if 73 #end if
74 #if $full_ext.endswith("gz") 74 #if $full_ext.endswith("gz")
75 zcat '$inputs.in.raw_in.in_f' > 'in_f' && 75 zcat '$inputs.in.raw_in.in_f' > 'in_f' &&
76 zcat '$inputs.in.raw_in.in_r' > 'in_r' && 76 zcat '$inputs.in.raw_in.in_r' > 'in_r' &&
77 #set file_path="-1 in_f -2 in_r"
78 #else if $full_ext.endswith("bz2") 77 #else if $full_ext.endswith("bz2")
79 bzcat '$inputs.in.raw_in.in_f' > 'in_f' && 78 bzcat '$inputs.in.raw_in.in_f' > 'in_f' &&
80 bzcat '$inputs.in.raw_in.in_r' > 'in_r' && 79 bzcat '$inputs.in.raw_in.in_r' > 'in_r' &&
81 #set file_path="-1 in_f -2 in_r" 80 #set file_path="-1 in_f -2 in_r"
81 ln -s '$inputs.in.raw_in.in_f' 'in_f' &&
82 ln -s '$inputs.in.raw_in.in_r' 'in_r' &&
83 #end if
84 ## paired data has by default no special treatment, i.e. it is given as comma separated list
85 ## except iff paired subsampling where -1 and -2 must be used
86 #if $subsample.selector == 'paired'
87 #set file_path="-1 in_f -2 in_r"
82 #else 88 #else
83 #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r) 89 #set file_path="in_f,in_r"
84 #end if 90 #end if
85 #else if $inputs.in.raw_in.selector == "paired_collection" 91 #else if $inputs.in.raw_in.selector == "paired_collection"
86 #set full_ext=$inputs.in.raw_in.in.forward.ext 92 #set full_ext=$inputs.in.raw_in.in.forward.ext
87 #if $full_ext != $inputs.in.raw_in.in.reverse.ext 93 #if $full_ext != $inputs.in.raw_in.in.reverse.ext
88 echo "Different datatypes for input paired-end files" && 94 echo "Different datatypes for input paired-end files" &&
89 exit 1 95 exit 1
90 #end if 96 #end if
91 #if $full_ext.endswith("gz") 97 #if $full_ext.endswith("gz")
92 zcat '$inputs.in.raw_in.in.forward' > 'in_f' && 98 zcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
93 zcat '$inputs.in.raw_in.in.reverse' > 'in_r' && 99 zcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
94 #set file_path="-1 in_f -2 in_r"
95 #else if $full_ext.endswith("bz2") 100 #else if $full_ext.endswith("bz2")
96 bzcat '$inputs.in.raw_in.in.forward' > 'in_f' && 101 bzcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
97 bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' && 102 bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
103 #else
104 ln -s '$inputs.in.raw_in.in.forward' 'in_f' &&
105 ln -s '$inputs.in.raw_in.in.reverse' 'in_r' &&
106 #end if
107 #if $subsample.selector == 'paired'
98 #set file_path="-1 in_f -2 in_r" 108 #set file_path="-1 in_f -2 in_r"
99 #else 109 #else
100 #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r) 110 #set file_path="in_f,in_r"
101 #end if 111 #end if
102 #end if 112 #end if
103 113
104 #if $full_ext.startswith("fastq") 114 #if $full_ext.startswith("fastq")
105 #set ext='fastq' 115 #set ext='fastq'
981 </output_collection> 991 </output_collection>
982 <assert_stderr> 992 <assert_stderr>
983 <has_text text="Downloading" negate="true"/> 993 <has_text text="Downloading" negate="true"/>
984 </assert_stderr> 994 </assert_stderr>
985 </test> 995 </test>
996 <!-- Paired fastq file as collection, Cached db -->
997 <test expect_num_outputs="4">
998 <section name="inputs">
999 <conditional name="in">
1000 <param name="selector" value="raw"/>
1001 <conditional name="raw_in">
1002 <param name="selector" value="paired_collection"/>
1003 <param name="in">
1004 <collection type="paired" name="pair">
1005 <element name="forward" value="SRS014464-Anterior_nares_mini.fastq" />
1006 <element name="reverse" value="SRS014464-Anterior_nares_mini.fastq" />
1007 </collection>
1008 </param>
1009 </conditional>
1010 <param name="read_min_len" value="70"/>
1011 <section name="mapping">
1012 <param name="bt2_ps" value="sensitive"/>
1013 <param name="min_mapq_val" value="5"/>
1014 </section>
1015 </conditional>
1016 <conditional name="db">
1017 <param name="db_selector" value="cached"/>
1018 <param name="cached_db" value="test-db-20210409"/>
1019 </conditional>
1020 </section>
1021 <section name="analysis">
1022 <conditional name="analysis_type">
1023 <param name="t" value="rel_ab"/>
1024 <conditional name="tax_lev">
1025 <param name="tax_lev" value="a"/>
1026 <param name="split_levels" value="false"/>
1027 </conditional>
1028 </conditional>
1029 <param name="min_cu_len" value="2000"/>
1030 <param name="organism_profiling" value="add_viruses"/>
1031 <param name="stat" value="avg_g"/>
1032 <param name="stat_q" value="0.2"/>
1033 <param name="perc_nonzero" value="0.33"/>
1034 <param name="avoid_disqm" value="true"/>
1035 </section>
1036 <conditional name="subsample">
1037 <param name="selector" value="no"/>
1038 </conditional>
1039 <section name="out">
1040 <param name="sample_id_key" value="SampleID"/>
1041 <param name="sample_id" value="Metaphlan_Analysis"/>
1042 <param name="use_group_representative" value="false"/>
1043 <param name="legacy_output" value="false"/>
1044 <param name="CAMI_format_output" value="false"/>
1045 <param name="unclassified_estimation" value="false"/>
1046 <param name="krona_output" value="false"/>
1047 </section>
1048 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
1049 <assert_contents>
1050 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1051 <has_text text="relative_abundance"/>
1052 <has_text text="NCBI_tax_id"/>
1053 <has_text text="clade_name"/>
1054 </assert_contents>
1055 </output>
1056 <output name="bowtie2out" ftype="tabular">
1057 <assert_contents>
1058 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
1059 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
1060 </assert_contents>
1061 </output>
1062 <output name="sam_output_file" ftype="sam">
1063 <assert_contents>
1064 <has_size min="8450" max="8550"/>
1065 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
1066 </assert_contents>
1067 </output>
1068 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
1069 <assert_contents>
1070 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1071 </assert_contents>
1072 </output>
1073 <assert_stderr>
1074 <has_text text="Downloading" negate="true"/>
1075 </assert_stderr>
1076 </test>
986 <!-- SAM, cached DB --> 1077 <!-- SAM, cached DB -->
987 <test expect_num_outputs="2"> 1078 <test expect_num_outputs="2">
988 <section name="inputs"> 1079 <section name="inputs">
989 <conditional name="in"> 1080 <conditional name="in">
990 <param name="selector" value="sam"/> 1081 <param name="selector" value="sam"/>