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comparison humann2.xml @ 4:fdec83ce1122 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:52:29 +0000
parents f22f41112336
children
comparison
equal deleted inserted replaced
3:f22f41112336 4:fdec83ce1122
1 <tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.2"> 1 <tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.3">
2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description> 2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
3 <macros> 3 <macros>
4 <import>humann2_macros.xml</import> 4 <import>humann2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="stdio"/> 6 <expand macro="stdio"/>
48 --pkl_output 'ref_db/metadata.pkl' 48 --pkl_output 'ref_db/metadata.pkl'
49 && 49 &&
50 #end if 50 #end if
51 #end if 51 #end if
52 52
53 #if $input.ext.startswith("fasta")
54 #set ext="fasta"
55 #else if $input.ext.startswith("fastq")
56 #set ext="fastq"
57 #else if $input.ext.endswith("bam")
58 #set ext="bam"
59 #else if $input.ext == 'sam'
60 #set ext="sam"
61 #else if $input.ext == 'biom1'
62 #set ext="biom"
63 #else
64 >&2 "unknown extension $input.ext"
65 exit 1;
66 #end if
67
68 #if $input.ext.endswith(".gz")
69 #set ext+=".gz"
70 #end if
71
53 humann2 72 humann2
54 --input '$input' 73 --input '$input'
74 --input-format $ext
55 -o 'output' 75 -o 'output'
56 $bypass.bypass_prescreen 76 $bypass.bypass_prescreen
57 $bypass.bypass_nucleotide_index 77 $bypass.bypass_nucleotide_index
58 $bypass.bypass_translated_search 78 $bypass.bypass_translated_search
59 $bypass.bypass_nucleotide_search 79 $bypass.bypass_nucleotide_search
109 --output-basename 'humann2' 129 --output-basename 'humann2'
110 $adv.remove_statified_output 130 $adv.remove_statified_output
111 $adv.remove_column_description_output 131 $adv.remove_column_description_output
112 ]]></command> 132 ]]></command>
113 <inputs> 133 <inputs>
114 <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/> 134 <param argument="--input" type="data" format="fastq,fastq.gz,fasta,fasta.gz,sam,bam,biom1" label="Input sequence file"/>
115 <section name="bypass" title="Options to bypass some steps" expanded="False"> 135 <section name="bypass" title="Options to bypass some steps" expanded="False">
116 <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/> 136 <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
117 <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/> 137 <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
118 <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/> 138 <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
119 <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/> 139 <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>
281 <has_text text="UNINTEGRATED" /> 301 <has_text text="UNINTEGRATED" />
282 </assert_contents> 302 </assert_contents>
283 </output> 303 </output>
284 </test> 304 </test>
285 <test> 305 <test>
286 <param name="input" value="input_sequences.fasta"/> 306 <param name="input" value="input_sequences.fastq.gz"/>
287 <param name="bypass_prescreen" value=""/> 307 <param name="bypass_prescreen" value=""/>
288 <param name="bypass_nucleotide_index" value=""/> 308 <param name="bypass_nucleotide_index" value=""/>
289 <param name="bypass_translated_search" value=""/> 309 <param name="bypass_translated_search" value=""/>
290 <param name="bypass_nucleotide_search" value=""/> 310 <param name="bypass_nucleotide_search" value=""/>
291 <param name="nucleotide_db_selector" value="history"/> 311 <param name="nucleotide_db_selector" value="history"/>