| Previous changeset 3:dde3036465de (2018-10-26) Next changeset 5:6d490b72aefa (2018-10-29) |
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Commit message:
planemo upload |
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added:
data_path.py data_path.xml filler.py filler.xml prince_postprocess.py prince_postprocess.xml |
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| diff -r dde3036465de -r 82569b47df8d data_path.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_path.py Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +import sys +import argparse as ap + +parser = ap.ArgumentParser(prog='data_path', conflict_handler='resolve', + description="Output the galaxy file path of datasets in a text file") + +input = parser.add_argument_group('Input', '') +input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to data1") +input.add_argument('-j', '--input2', nargs='*', required=True, help="Paths to data2") + +if len(sys.argv) == 0: + parser.print_usage() + sys.exit(1) + +args = parser.parse_args() +output = open('paths.txt', 'w') +if len(args.input2) == 0: + for index,path in enumerate(args.input): + output.write("%s\n" % (path)) +else: + for index,path in enumerate(args.input): + output.write("%s\t%s\n" % (path, args.input2[index])) |
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| diff -r dde3036465de -r 82569b47df8d data_path.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_path.xml Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,17 @@ +<tool id="data_path" name="Data Path" version="1.0.0"> + <description>creates a txt file of the paths of items in a data collection</description> + <command interpreter="python"><![CDATA[ + data_path.py -i #for $path in $paths# $path.forward #end for# -j #for $path in $paths# $path.reverse #end for# + ]]></command> + <inputs> + <param name="paths" type="data_collection" format="data" label="Collection of files" help="" optional="False" multiple="True"/> + </inputs> + <outputs> + <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> + </outputs> + <help> +This tool outputs the paths of the files in a data collection + </help> + <citations> + </citations> +</tool> |
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| diff -r dde3036465de -r 82569b47df8d filler.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filler.py Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,20 @@ +#!/usr/bin/env python + +import sys +import argparse as ap + +parser = ap.ArgumentParser(prog='filler', conflict_handler='resolve', + description="produce filler collection to deal with galaxy handling") + +input = parser.add_argument_group('Input', '') +input.add_argument('-i', '--input', nargs=1, required=True, help="Paths to forward reads") +input.add_argument('-o', '--output', nargs=1, required=True, help="output") + +if len(sys.argv) == 0: + parser.print_usage() + sys.exit(1) + +args = parser.parse_args() +output = open(args.output[0], 'w') +output.write(args.input[0]) +output.write("\n") |
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| diff -r dde3036465de -r 82569b47df8d filler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filler.xml Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,36 @@ +<tool id="filler" name="Filler" version="1.0.0"> + <description>Filler Function to deal with paired collection</description> + <command interpreter="python"><![CDATA[ + filler.py + #if str( $data_input.data_selector ) == "paired" + -i $data_input.input1.forward.element_identifier + #end if + #if str( $data_input.data_selector ) == "single" + -i "$data_input.input2.element_identifier" + #end if + + -o $output + ]]></command> + <inputs> + <conditional name="data_input"> + <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/> + </when> + <when value="single"> + <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" type="data_collection"/> + </outputs> + <help> +This tool processes the PRINCE galaxy output such that it is in line with the command line + </help> + <citations> + </citations> +</tool> |
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| diff -r dde3036465de -r 82569b47df8d prince_postprocess.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prince_postprocess.py Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,36 @@ +#!/usr/bin/env python + +import sys +import argparse as ap +import re +parser = ap.ArgumentParser(prog='prince_postprocess', conflict_handler='resolve', + description="Postprocess galaxy PRINCE output") + +input = parser.add_argument_group('Input', '') +input.add_argument('-i', '--input', nargs=1, required=True, help="PRINCE OUTPUT") +input.add_argument('-s', '--sample', nargs='*', required=True, help="Sample names") + +if len(sys.argv) == 0: + parser.print_usage() + sys.exit(1) + +args = parser.parse_args() + +#print(args.input) +#sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.label.rstrip().lstrip()) + +with open(args.input[0]) as prince_output: + with open('prince_postprocess_output.txt', 'w') as output: + x = 1 + index = 0 + for line in prince_output: + if x%2 == 0: + sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index]) + output.write(re.sub('.*.dat', sample, line)) + index += 1 + else: + output.write(line) + x += 1 + #output.write("\n") + + |
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| diff -r dde3036465de -r 82569b47df8d prince_postprocess.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prince_postprocess.xml Mon Oct 29 07:52:12 2018 -0400 |
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| @@ -0,0 +1,18 @@ +<tool id="prince_postprocess" name="Prince Postprocess" version="1.0.0"> + <description>Postprocess PRINCE galaxy output</description> + <command interpreter="python"><![CDATA[ + prince_postprocess.py -i $prince_output -s #for $path in $paths# $path.element_identifier #end for# + ]]></command> + <inputs> + <param name="paths" type="data" format="data" label="Collection of files" help="" optional="False" multiple="True"/> + <param name="prince_output" format="txt" type="data" label="PRINCE output" /> + </inputs> + <outputs> + <data name="output" format="txt" from_work_dir="prince_postprocess_output.txt"/> + </outputs> + <help> +This tool processes the PRINCE galaxy output such that it is in line with the command line + </help> + <citations> + </citations> +</tool> |