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comparison amplicon_analysis_pipeline.xml @ 1:1c1902e12caf draft

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Updated to version 1.2.1.0
author pjbriggs
date Wed, 25 Apr 2018 03:54:00 -0400
parents 47ec9c6f44b8
children 43d6f81bc667
comparison
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0:47ec9c6f44b8 1:1c1902e12caf
1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.0.6"> 1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.1.0">
2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> 2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1">amplicon_analysis_pipeline</requirement> 4 <requirement type="package" version="1.2.1">amplicon_analysis_pipeline</requirement>
5 <requirement type="package" version="1.11">cutadapt</requirement> 5 <requirement type="package" version="1.11">cutadapt</requirement>
6 <requirement type="package" version="1.33">sickle</requirement> 6 <requirement type="package" version="1.33">sickle</requirement>
7 <requirement type="package" version="27-08-2013">bioawk</requirement> 7 <requirement type="package" version="27-08-2013">bioawk</requirement>
8 <requirement type="package" version="2.8.1">pandaseq</requirement> 8 <requirement type="package" version="2.8.1">pandaseq</requirement>
9 <requirement type="package" version="3.5.0">spades</requirement> 9 <requirement type="package" version="3.5.0">spades</requirement>
20 <stdio> 20 <stdio>
21 <exit_code range="1:" /> 21 <exit_code range="1:" />
22 </stdio> 22 </stdio>
23 <command><![CDATA[ 23 <command><![CDATA[
24 ## Set the reference database name 24 ## Set the reference database name
25 #if $reference_database == "" 25 #if $reference_database == "-S"
26 #set reference_database_name = "silva"
27 #else if $reference_database == "-H"
28 #set reference_database_name = "homd"
29 #else
26 #set reference_database_name = "gg" 30 #set reference_database_name = "gg"
27 #else
28 #set reference_database_name = "silva"
29 #end if 31 #end if
30 32
31 ## Run the amplicon analysis pipeline wrapper 33 ## Run the amplicon analysis pipeline wrapper
32 python $__tool_directory__/amplicon_analysis_pipeline.py 34 python $__tool_directory__/amplicon_analysis_pipeline.py
33 ## Set options 35 ## Set options
50 -L $minimum_length 52 -L $minimum_length
51 #end if 53 #end if
52 -P $pipeline 54 -P $pipeline
53 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH 55 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
54 #if str( $reference_database ) != "" 56 #if str( $reference_database ) != ""
55 "${reference_database}" 57 ${reference_database}
56 #end if 58 #end if
57 #if str($categories_file_in) != 'None' 59 #if str($categories_file_in) != 'None'
58 -c "${categories_file_in}" 60 -c "${categories_file_in}"
59 #end if 61 #end if
60 ## Input files 62 ## Input files
184 </param> 186 </param>
185 <param type="select" name="reference_database" 187 <param type="select" name="reference_database"
186 label="Reference database"> 188 label="Reference database">
187 <option value="" selected="true">GreenGenes</option> 189 <option value="" selected="true">GreenGenes</option>
188 <option value="-S">Silva</option> 190 <option value="-S">Silva</option>
191 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
189 </param> 192 </param>
190 </inputs> 193 </inputs>
191 <outputs> 194 <outputs>
192 <data format="tabular" name="metatable_mod" 195 <data format="tabular" name="metatable_mod"
193 label="${tool.name}:${title} Metatable_mod.txt" /> 196 label="${tool.name}:${title} Metatable_mod.txt" />