# HG changeset patch
# User bebatut
# Date 1460726121 14400
# Node ID 31394a0c024266a8acef160deb15fd17c3ec6739
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
diff -r 000000000000 -r 31394a0c0242 combine_metaphlan2_humann2.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/combine_metaphlan2_humann2.py Fri Apr 15 09:15:21 2016 -0400
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+
+def extract_clade_abundance(metaphlan2_filepath):
+ clade_abundance = {}
+ with open(metaphlan2_filepath, 'r') as metaphlan2_file:
+ for line in metaphlan2_file.readlines():
+ if line.find('g__') == -1:
+ continue
+
+ split_line = line[:-1].split('\t')
+ taxo = split_line[0]
+ abundance = split_line[1]
+
+ genus = taxo[(taxo.find('g__')+3):]
+ if genus.find('|') != -1:
+ genus = genus[:(genus.find('|'))]
+ clade_abundance.setdefault(genus, {'abundance':0, 'species':{}})
+ if taxo.find('t__') != -1:
+ continue
+ elif taxo.find('s__') != -1:
+ species = taxo[(taxo.find('s__')+3):]
+ clade_abundance[genus]['species'].setdefault(species, abundance)
+ else:
+ clade_abundance[genus]['abundance'] = abundance
+ return clade_abundance
+
+def compute_overall_abundance(humann2_file):
+ overall_abundance = 0
+ with open(args.humann2_file, 'r') as humann2_file:
+ for line in humann2_file.readlines():
+ if line.find('|') != -1 or line.startswith('#'):
+ continue
+ split_line = line[:-1].split('\t')
+ overall_abundance += float(split_line[1])
+ return overall_abundance
+
+def format_characteristic_name(name):
+ formatted_name = name
+ formatted_name = formatted_name.replace('/',' ')
+ formatted_name = formatted_name.replace('-',' ')
+ formatted_name = formatted_name.replace("'",'')
+ if formatted_name.find('(') != -1 and formatted_name.find(')') != -1:
+ open_bracket = formatted_name.find('(')
+ close_bracket = formatted_name.find(')')+1
+ formatted_name = formatted_name[:open_bracket] + formatted_name[close_bracket:]
+ return formatted_name
+
+def combine_metaphlan2_humann2(args):
+ clade_abundance = extract_clade_abundance(args.metaphlan2_file)
+ overall_abundance = compute_overall_abundance(args.humann2_file)
+
+ with open(args.output_file, 'w') as output_file:
+ output_file.write('genus\t')
+ output_file.write('genus_abundance\t')
+ output_file.write('species\t')
+ output_file.write('species_abundance\t')
+ output_file.write(args.type + '_id\t')
+ output_file.write(args.type + '_name\t')
+ output_file.write(args.type + '_abundance\n')
+ with open(args.humann2_file, 'r') as humann2_file:
+ for line in humann2_file.readlines():
+ if line.find('|') == -1:
+ continue
+
+ split_line = line[:-1].split('\t')
+ abundance = 100*float(split_line[1])/overall_abundance
+ annotation = split_line[0].split('|')
+ characteristic = annotation[0].split(':')
+ characteristic_id = characteristic[0]
+ characteristic_name = ''
+ if len(characteristic) > 1:
+ characteristic_name = format_characteristic_name(characteristic[-1])
+ taxo = annotation[1].split('.')
+
+ if taxo[0] == 'unclassified':
+ continue
+ genus = taxo[0][3:]
+ species = taxo[1][3:]
+
+ if not clade_abundance.has_key(genus):
+ print "no", genus, "found in", args.metaphlan2_file
+ continue
+ if not clade_abundance[genus]['species'].has_key(species):
+ print "no", species, "found in", args.metaphlan2_file,
+ print "for", genus
+ continue
+ output_file.write(genus + '\t')
+ output_file.write(clade_abundance[genus]['abundance'] + '\t')
+ output_file.write(species + '\t')
+ output_file.write(clade_abundance[genus]['species'][species] + '\t')
+ output_file.write(characteristic_id + '\t')
+ output_file.write(characteristic_name + '\t')
+ output_file.write(str(abundance) + '\n')
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--humann2_file', required=True)
+ parser.add_argument('--metaphlan2_file', required=True)
+ parser.add_argument('--output_file', required=True)
+ parser.add_argument('--type', required=True,
+ choices = ['gene_families','pathways'])
+ args = parser.parse_args()
+
+ combine_metaphlan2_humann2(args)
\ No newline at end of file
diff -r 000000000000 -r 31394a0c0242 combine_metaphlan2_humann2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/combine_metaphlan2_humann2.xml Fri Apr 15 09:15:21 2016 -0400
@@ -0,0 +1,74 @@
+<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0">
+ <description>to relate genus/species abundances and gene families/pathways abundances</description>
+
+ <requirements>
+ </requirements>
+
+ <stdio>
+ <exit_code range="1:" />
+ <exit_code range=":-1" />
+ </stdio>
+
+ <version_command></version_command>
+
+ <command><![CDATA[
+ python $__tool_directory__/combine_metaphlan2_humann2.py
+ --metaphlan2_file $metaphlan2_file
+ --humann2_file $humann2_file
+ --type $type
+
+ #if str($type) == 'gene_families'
+ --output_file $gene_families_output_file
+ #else
+ --output_file $pathway_output_file
+ #end if
+ ]]></command>
+
+ <inputs>
+ <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/>
+
+ <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/>
+
+ <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)">
+ <option value="gene_families" selected="true">Gene families</option>
+ <option value="pathways">Pathways</option>
+ </param>
+ </inputs>
+
+ <outputs>
+ <data name="gene_families_output_file" format="tabular"
+ label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" >
+ <filter>type=="gene_families"</filter>
+ </data>
+ <data name="pathway_output_file" format="tabular"
+ label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" >
+ <filter>type=="pathways"</filter>
+ </data>
+ </outputs>
+
+ <tests>
+ <test>
+ <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
+ <param name="humann2_file" value="humann2_gene_families_input.tabular"/>
+ <param name='type' value="gene_families"/>
+ <output name="gene_families_output_file" file="gene_families_output.tabular"/>
+ </test>
+ <test>
+ <param name="metaphlan2_file" value="metaphlan2_input.txt"/>
+ <param name="humann2_file" value="humann2_pathways_input.tabular"/>
+ <param name='type' value="pathways"/>
+ <output name="pathway_output_file" file="pathways_output.tabular"/>
+ </test>
+ </tests>
+
+ <help><![CDATA[
+**What it does**
+
+This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs.
+
+For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus.
+ ]]></help>
+
+ <citations>
+ </citations>
+</tool>