# HG changeset patch
# User czouaoui
# Date 1521534337 14400
# Node ID 10eedb4b587f32b7c90f93058df2719853857c1f
# Parent  5ac3be5b1d1279b3e0cc3dbbeca4dd65deaa4e29
Deleted selected files

diff -r 5ac3be5b1d12 -r 10eedb4b587f abundanceTable_to_biom/abundanceTable_to_biom.py~
--- a/abundanceTable_to_biom/abundanceTable_to_biom.py~	Tue Mar 20 04:21:57 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-import datetime
-import argparse
-import csv
-import json
-
-def __main__():
-    print "Generating biom file ..."
-    options = argsParser()
-    families, samples, data = abundanceTableParser(options.file)
-    biom_file = constructBiom(families, samples, data)
-    file_name = options.out_name + '.biom' if options.out_name else 'result.biom'
-    with open(file_name, 'w') as output:
-    	json.dump(biom_file, output)
-    print "Your biom file (" + file_name + ") is now created"
-
-def argsParser():
-    parser = argparse.ArgumentParser()
-    parser.add_argument("-f", "--file", type=argparse.FileType('r'), help="Abundance table in csv format")
-    parser.add_argument("-o", "--out_name", help="BIOM (v1.0) file name")
-
-    return parser.parse_args()
-
-def abundanceTableParser(file):
-    with file:
-        reader = csv.reader(file)
-
-	families = []
-        for i, row in enumerate(reader):
-	    if i != 0:
-                families.append({"id":"OTU_" + str(i), "metadata":{"taxonomy":["k__", "p__", "c__", "o__", 
-		"f__" + row[0], "g__", "s__"]}})
-
-	file.seek(0)
-	first_row = next(reader)
-	samples = []
-        for i in range(1, len(first_row)):
-            samples.append({"id":first_row[i], "metadata":{"phinchID":first_row[i]}})
-
-	file.seek(0)
-	data = []
-        for i, row in enumerate(reader):
-	    if i != 0:
-		for j in range(1, len(row)):
-	            if row[j] != 'NA':
-		    	data.append([i - 1, j - 1, int(row[j])])
-    
-    return families, samples, data
-
-def constructBiom(families, samples, data):
-    biom = {"id":"null",
-	    "format": "Biological Observation Matrix 0.9.1-dev",
-            "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html",
-            "type": "OTU table",
-            "generated_by": "abundanceTable_to_biom script",
- 	    "date": datetime.date.today().isoformat(),
- 	    "matrix_type": "sparse",
- 	    "matrix_element_type": "int",
- 	    "shape": [len(families), len(samples)],
-	    "rows":families,
-            "columns":samples,
-            "data":data}
-    return biom
-    
-
-if __name__ == "__main__":
-    __main__()
diff -r 5ac3be5b1d12 -r 10eedb4b587f abundanceTable_to_biom/abundanceTable_to_biom.xml
--- a/abundanceTable_to_biom/abundanceTable_to_biom.xml	Tue Mar 20 04:21:57 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0">
-    <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result
-    ]]></command>
-    <inputs>
-        <param type="data" name="input" format="csv" label="Abundance table"/>
-    </inputs>
-    <outputs>
-        <data name= "output" format="biom" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" format="csv" value="merge_summary_reads.csv"/>
-            <output name="output" format="biom" file="biom_result.biom"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        This tool is used to generate a Biom file (v1.0) from an abundance table. 
-	The first column of the header is a taxonomy list (families). Next columns contain sample ids.
-	The abundancy of reads is set inside the table. 
-    ]]></help>
-</tool>
diff -r 5ac3be5b1d12 -r 10eedb4b587f abundanceTable_to_biom/abundanceTable_to_biom.xml~
--- a/abundanceTable_to_biom/abundanceTable_to_biom.xml~	Tue Mar 20 04:21:57 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0">
-    <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result
-    ]]></command>
-    <inputs>
-        <param type="data" name="input" format="csv" label="Abundance table"/>
-    </inputs>
-    <outputs>
-        <data name= "output" format="biom" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" format="csv" value="merge_summary_reads.csv"/>
-            <output name="output" format="biom" file="biom_result.biom"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        This tool is used to generate a Biom file (v1.0) from an abundance table. 
-	The first column of the header is a taxonomy list (families). Next columns contain sample ids.
-	The abundancy of reads is set inside the table. 
-    ]]></help>
-</tool>