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comparison metaphlan2.xml @ 1:9be4beda6482 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author iuc
date Fri, 19 Mar 2021 09:38:42 +0000
parents 8c82c4d90cc6
children f60773e921fa
comparison
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0:8c82c4d90cc6 1:9be4beda6482
1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0"> 1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1">
2 2
3 <description>to profile the composition of microbial communities</description> 3 <description>to profile the composition of microbial communities</description>
4 4
5 <macros> 5 <macros>
6 <import>metaphlan2_macros.xml</import> 6 <import>metaphlan2_macros.xml</import>
8 8
9 <expand macro="requirements"> 9 <expand macro="requirements">
10 <requirement type="package" version="2.3.0">bowtie2</requirement> 10 <requirement type="package" version="2.3.0">bowtie2</requirement>
11 <requirement type="package" version="2.7.10">python</requirement> 11 <requirement type="package" version="2.7.10">python</requirement>
12 </expand> 12 </expand>
13 13
14 <expand macro="stdio"/> 14 <expand macro="stdio"/>
15 15
16 <version_command> 16 <version_command>metaphlan2.py -v</version_command>
17 <![CDATA[
18 metaphlan2.py -v
19 ]]>
20 </version_command>
21 17
22 <command> 18 <command><![CDATA[
23 <![CDATA[ 19 #if $db.db_selector == "history"
24 #if $db.db_selector == "history" 20 mkdir ref_db
25 mkdir ref_db 21 &&
26 && 22 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
27 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db' 23 &&
28 && 24 python '$__tool_directory__/transform_json_to_pkl.py'
29 python '$__tool_directory__/transform_json_to_pkl.py' 25 --json_input '$db.mpa_pkl'
30 --json_input '$db.mpa_pkl' 26 --pkl_output 'ref_db/metadata.pkl'
31 --pkl_output 'ref_db/metadata.pkl' 27 &&
32 && 28 #end if
33 #end if
34 29
35 metaphlan2.py 30 #if $input_file.datatype.file_ext.startswith("fastq")
36 '$input_file' 31 #set ext='fastq'
37 -o '$output_file' 32 #else
38 --input_type '${input_file.datatype.file_ext}' 33 #set ext=$input_file.datatype.file_ext
39 --bowtie2_exe `which bowtie2` 34 #end if
40 35
41 #if $db.db_selector == "cached" 36 metaphlan2.py
42 #set $path = $db.cached_db.fields.path 37 '$input_file'
43 #set $value = $db.cached_db.fields.value 38 -o '$output_file'
44 --bowtie2db $path/$value 39 --input_type $ext
45 --mpa_pkl $path/$value'.pkl' 40 --bowtie2_exe `which bowtie2`
46 #else
47 --bowtie2db 'ref_db/ref_db'
48 --mpa_pkl 'ref_db/metadata.pkl'
49 #end if
50 41
51 --no_map 42 #if $db.db_selector == "cached"
43 #set $path = $db.cached_db.fields.path
44 #set $value = $db.cached_db.fields.value
45 --bowtie2db $path/$value
46 --mpa_pkl $path/$value'.pkl'
47 #else
48 --bowtie2db 'ref_db/ref_db'
49 --mpa_pkl 'ref_db/metadata.pkl'
50 #end if
52 51
53 -t '$analysis_type.analysis_type_select' 52 --no_map
54 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
55 --tax_lev '$analysis_type.tax_lev'
56 #else if $analysis_type.analysis_type_select == "marker_ab_table"
57 --nreads '$analysis_type.nreads'
58 #else if $analysis_type.analysis_type_select == "marker_pres_table"
59 --pres_th '$analysis_type.pres_th'
60 #end if
61 53
62 --min_cu_len '$min_cu_len' 54 -t '$analysis_type.analysis_type_select'
63 --min_alignment_len '$min_alignment_len' 55 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
56 --tax_lev '$analysis_type.tax_lev'
57 #else if $analysis_type.analysis_type_select == "marker_ab_table"
58 --nreads '$analysis_type.nreads'
59 #else if $analysis_type.analysis_type_select == "marker_pres_table"
60 --pres_th '$analysis_type.pres_th'
61 #end if
64 62
65 $ignore_viruses 63 --min_cu_len '$min_cu_len'
66 $ignore_eukaryotes 64 --min_alignment_len '$min_alignment_len'
67 $ignore_bacteria
68 $ignore_archaea
69 65
70 --stat_q '$stat_q' 66 $ignore_viruses
71 -s '$sam_output_file' 67 $ignore_eukaryotes
72 --biom '$biom_output_file' 68 $ignore_bacteria
73 ]]> 69 $ignore_archaea
74 </command> 70
71 --stat_q '$stat_q'
72 -s '$sam_output_file'
73 --biom '$biom_output_file'
74 ]]></command>
75 75
76 <inputs> 76 <inputs>
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/> 77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
78 <conditional name="db"> 78 <conditional name="db">
79 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> 79 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
124 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/> 124 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
125 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/> 125 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
126 </inputs> 126 </inputs>
127 127
128 <outputs> 128 <outputs>
129 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> 129 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" />
130 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> 130 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" />
131 <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" /> 131 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
132 </outputs> 132 </outputs>
133 133
134 <tests> 134 <tests>
135 <test> 135 <test>
136 <param name="input_file" value="input_sequences.fasta"/> 136 <param name="input_file" value="input_sequences.fasta"/>