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comparison metaphlan2.xml @ 1:f279fc0892fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
author iuc
date Wed, 05 Jul 2017 07:40:16 -0400
parents a12c7f019bdf
children 5b7ee956d89b
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0:a12c7f019bdf 1:f279fc0892fc
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 '$db.mpa_pkl' 26 --pkl_output 'ref_db/metadata.pkl'
31 --pkl_output 'ref_db/metadata.pkl' 27 &&
32 && 28 #end if
33 #end if
34 29
35 metaphlan2.py 30 metaphlan2.py
36 '$input_file' 31 '$input_file'
37 -o '$output_file' 32 -o '$output_file'
38 --input_type '${input_file.datatype.file_ext}' 33 --input_type '${input_file.datatype.file_ext}'
39 --bowtie2_exe `which bowtie2` 34 --bowtie2_exe `which bowtie2`
40 35
41 #if $db.db_selector == "cached" 36 #if $db.db_selector == "cached"
42 #set $path = $db.cached_db.fields.path 37 #set $path = $db.cached_db.fields.path
43 #set $value = $db.cached_db.fields.value 38 #set $value = $db.cached_db.fields.value
44 --bowtie2db $path/$value 39 --bowtie2db $path/$value
45 --mpa_pkl $path/$value'.pkl' 40 --mpa_pkl $path/$value'.pkl'
46 #else 41 #else
47 --bowtie2db 'ref_db/ref_db' 42 --bowtie2db 'ref_db/ref_db'
48 --mpa_pkl 'ref_db/metadata.pkl' 43 --mpa_pkl 'ref_db/metadata.pkl'
49 #end if 44 #end if
50 45
51 --no_map 46 --no_map
52 47
53 -t '$analysis_type.analysis_type_select' 48 -t '$analysis_type.analysis_type_select'
54 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats" 49 #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' 50 --tax_lev '$analysis_type.tax_lev'
56 #else if $analysis_type.analysis_type_select == "marker_ab_table" 51 #else if $analysis_type.analysis_type_select == "marker_ab_table"
57 --nreads '$analysis_type.nreads' 52 --nreads '$analysis_type.nreads'
58 #else if $analysis_type.analysis_type_select == "marker_pres_table" 53 #else if $analysis_type.analysis_type_select == "marker_pres_table"
59 --pres_th '$analysis_type.pres_th' 54 --pres_th '$analysis_type.pres_th'
60 #end if 55 #end if
61 56
62 --min_cu_len '$min_cu_len' 57 --min_cu_len '$min_cu_len'
63 --min_alignment_len '$min_alignment_len' 58 --min_alignment_len '$min_alignment_len'
64 59
65 $ignore_viruses 60 $ignore_viruses
66 $ignore_eukaryotes 61 $ignore_eukaryotes
67 $ignore_bacteria 62 $ignore_bacteria
68 $ignore_archaea 63 $ignore_archaea
69 64
70 --stat_q '$stat_q' 65 --stat_q '$stat_q'
71 -s '$sam_output_file' 66 -s '$sam_output_file'
72 --biom '$biom_output_file' 67 --biom '$biom_output_file'
73 ]]> 68 ]]></command>
74 </command>
75 69
76 <inputs> 70 <inputs>
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/> 71 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
78 <conditional name="db"> 72 <conditional name="db">
79 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> 73 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
124 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/> 118 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
125 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/> 119 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
126 </inputs> 120 </inputs>
127 121
128 <outputs> 122 <outputs>
129 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> 123 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" />
130 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> 124 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" />
131 <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" /> 125 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
132 </outputs> 126 </outputs>
133 127
134 <tests> 128 <tests>
135 <test> 129 <test>
136 <param name="input_file" value="input_sequences.fasta"/> 130 <param name="input_file" value="input_sequences.fasta"/>