Mercurial > repos > matnguyen > pathogist
changeset 1:c1b6f5fbbcad draft
Updated pathogist version
| author | matnguyen |
|---|---|
| date | Fri, 01 Feb 2019 16:56:03 -0500 |
| parents | 6a73638d707c |
| children | baf1e89b42eb |
| files | galaxy/tools/concatenator/concatenator galaxy/tools/concatenator/concatenator.xml galaxy/tools/consensus_clustering/consensus_clustering.xml galaxy/tools/correlation_clustering/correlation_clustering.xml galaxy/tools/distance/distance.xml galaxy/tools/visualization/visualization.xml tools/concatenator/concatenator tools/concatenator/concatenator.xml tools/consensus_clustering/consensus_clustering.xml tools/correlation_clustering/correlation_clustering.xml tools/distance/distance.xml tools/visualization/visualization.xml |
| diffstat | 12 files changed, 176 insertions(+), 176 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/concatenator/concatenator Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,21 @@ +#!/usr/bin/env python + +import sys +import argparse as ap + +parser = ap.ArgumentParser(prog='concatenater', conflict_handler='resolve', + description="Concatenates all accessions and their associated paths") + +input = parser.add_argument_group('Input', '') +input.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)") +input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls") + +if len(sys.argv) == 1: + parser.print_usage() + sys.exit(1) + +args = parser.parse_args() +output = open('paths.txt', 'w') + +for index,path in enumerate(args.input): + output.write("%s=%s\n" % (args.name[index], path))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/concatenator/concatenator.xml Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,27 @@ +<tool id="concatenator" name="Concatenator" version="1.0.0"> + <description>creates a list of accessions and the associated path to their variant calls</description> + <requirements> + <requirement type="package" version="0.2.3">pathogist</requirement> + </requirements> + + <command><![CDATA[ + $__tool_directory__/concatenator -n #for $path in $paths# ${path.element_identifier} #end for# + -i #for $path in $paths# $path #end for# + ]]></command> + + <inputs> + <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> + </inputs> + + <outputs> + <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> + </outputs> + + <help> + + </help> + + <citations> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/consensus_clustering/consensus_clustering.xml Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,34 @@ +<tool id="consensus_clustering" name="PathOGiST - Consensus Clustering" version="1.0.0"> + <description>: Performs consensus clustering on multiple clusterings</description> + <requirements> + <requirement type="package" version="0.2.3">pathogist</requirement> + </requirements> + + <command><![CDATA[ + PATHOGIST consensus $constraints $distances $clusterings $fine_clusterings cc.tsv + ]]></command> + + <inputs> + <param name="distances" type="data" format="tabular,txt" label="Distance Matrices" + help="File contains paths to distance matrices for different clusterings"/> + <param name="clusterings" type="data" format="tabular,txt" label="Clusterings" + help="File contains paths to clusterings (matrices or lists of clustering assignments)"/> + <param name="fine_clusterings" type="data" format="tabular,txt" label="Fine Clusterings" + help="File contains names of the clusterings which are the finest"/> + <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue="" + label="All constraints" + help="Add all constraints to the optimization problem, not just those with mixed signs"/> + </inputs> + + <outputs> + <data name="clustering" label="Consensus clustering on ${on_string}" format="tabular" from_work_dir="cc.tsv"/> + </outputs> + + <help> + + </help> + + <citations> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/correlation_clustering/correlation_clustering.xml Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,31 @@ +<tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0"> + <description>: Runs correlation clustering on a distance matrix file</description> + <requirements> + <requirement type="package" version="0.2.3">pathogist</requirement> + </requirements> + + <command><![CDATA[ + PATHOGIST correlation $constraints $distance $threshold cc.tsv + ]]></command> + + <inputs> + <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/> + <param name="threshold" type="integer" value="0" label="Threshold Value" + help="The threshold value can be determined by visualizing the distance matrix"/> + <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue="" + label="All Constraints" + help="Add all constraints to the optimization problem, not just those with mixed signs"/> + </inputs> + + <outputs> + <data name="clustering" label="Correlation clustering of ${on_string}" format="tabular" from_work_dir="cc.tsv"/> + </outputs> + + <help> + + </help> + + <citations> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/distance/distance.xml Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,32 @@ +<tool id="distance" name="PathOGiST - Distance" version="1.0.0"> + <description>: Construct distance matrix from genotyping data</description> + <requirements> + <requirement type="package" version="0.2.3">pathogist</requirement> + </requirements> + + <command><![CDATA[ + PATHOGIST distance $genotyping $data_type matrix.tsv + ]]></command> + + <inputs> + <param name="genotyping" type="data" format="tabular,txt" label="Calls" + help="File containing paths to signal calls"/> + <param name="data_type" type="select" label="Data Type"> + <option value="MLST" selected="True">MLST</option> + <option value="SNP">SNP</option> + <option value="CNV">CNV</option> + </param> + </inputs> + + <outputs> + <data name="matrix" label="Distance matrix of ${on_string}" format="tabular" from_work_dir="matrix.tsv"/> + </outputs> + + <help> + + </help> + + <citations> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/visualization/visualization.xml Fri Feb 01 16:56:03 2019 -0500 @@ -0,0 +1,31 @@ +<tool id="visualization" name="PathOGiST - Visualization" version="1.0.0"> + <description>: Visualize distance matrix</description> + <requirements> + <requirement type="package" version="0.2.3">pathogist</requirement> + </requirements> + + <command><![CDATA[ + PATHOGIST vis $distance $sample $pdf + ]]></command> + + <inputs> + <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/> + <param name="sample" type="text" size="30" value="sample" label="Sample Name"/> + <param name="pdf" type="boolean" checked="false" truevalue="--save_pdf vis.pdf" falsevalue="" label="Save PDF"/> + </inputs> + + <outputs> + <data name="diagram" label="Diagram of ${on_string}" format="png" from_work_dir="sample.png"/> + <data name="pdf_output" label="PDF of ${on_string}" format="pdf" from_work_dir="vis.pdf"> + <filter>pdf == True</filter> + </data> + </outputs> + + <help> + + </help> + + <citations> + + </citations> +</tool>
--- a/tools/concatenator/concatenator Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -#!/usr/bin/env python - -import sys -import argparse as ap - -parser = ap.ArgumentParser(prog='concatenater', conflict_handler='resolve', - description="Concatenates all accessions and their associated paths") - -input = parser.add_argument_group('Input', '') -input.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)") -input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls") - -if len(sys.argv) == 1: - parser.print_usage() - sys.exit(1) - -args = parser.parse_args() -output = open('paths.txt', 'w') - -for index,path in enumerate(args.input): - output.write("%s=%s\n" % (args.name[index], path))
--- a/tools/concatenator/concatenator.xml Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -<tool id="concatenator" name="Concatenator" version="1.0.0"> - <description>creates a list of accessions and the associated path to their variant calls</description> - <requirements> - <requirement type="package" version="0.0.1">pathogist</requirement> - </requirements> - - <command><![CDATA[ - $__tool_directory__/concatenator -n #for $path in $paths# ${path.element_identifier} #end for# - -i #for $path in $paths# $path #end for# - ]]></command> - - <inputs> - <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> - </inputs> - - <outputs> - <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> - </outputs> - - <help> - - </help> - - <citations> - - </citations> -</tool>
--- a/tools/consensus_clustering/consensus_clustering.xml Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -<tool id="consensus_clustering" name="PathOGiST - Consensus Clustering" version="1.0.0"> - <description>: Performs consensus clustering on multiple clusterings</description> - <requirements> - <requirement type="package" version="0.0.1">pathogist</requirement> - </requirements> - - <command><![CDATA[ - PATHOGIST consensus $constraints $distances $clusterings $fine_clusterings cc.tsv - ]]></command> - - <inputs> - <param name="distances" type="data" format="tabular,txt" label="Distance Matrices" - help="File contains paths to distance matrices for different clusterings"/> - <param name="clusterings" type="data" format="tabular,txt" label="Clusterings" - help="File contains paths to clusterings (matrices or lists of clustering assignments)"/> - <param name="fine_clusterings" type="data" format="tabular,txt" label="Fine Clusterings" - help="File contains names of the clusterings which are the finest"/> - <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue="" - label="All constraints" - help="Add all constraints to the optimization problem, not just those with mixed signs"/> - </inputs> - - <outputs> - <data name="clustering" label="Consensus clustering on ${on_string}" format="tabular" from_work_dir="cc.tsv"/> - </outputs> - - <help> - - </help> - - <citations> - - </citations> -</tool>
--- a/tools/correlation_clustering/correlation_clustering.xml Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -<tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0"> - <description>: Runs correlation clustering on a distance matrix file</description> - <requirements> - <requirement type="package" version="0.0.1">pathogist</requirement> - </requirements> - - <command><![CDATA[ - PATHOGIST correlation $constraints $distance $threshold cc.tsv - ]]></command> - - <inputs> - <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/> - <param name="threshold" type="integer" value="0" label="Threshold Value" - help="The threshold value can be determined by visualizing the distance matrix"/> - <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue="" - label="All Constraints" - help="Add all constraints to the optimization problem, not just those with mixed signs"/> - </inputs> - - <outputs> - <data name="clustering" label="Correlation clustering of ${on_string}" format="tabular" from_work_dir="cc.tsv"/> - </outputs> - - <help> - - </help> - - <citations> - - </citations> -</tool>
--- a/tools/distance/distance.xml Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -<tool id="distance" name="PathOGiST - Distance" version="1.0.0"> - <description>: Construct distance matrix from genotyping data</description> - <requirements> - <requirement type="package" version="0.0.1">pathogist</requirement> - </requirements> - - <command><![CDATA[ - PATHOGIST distance $genotyping $data_type matrix.tsv - ]]></command> - - <inputs> - <param name="genotyping" type="data" format="tabular,txt" label="Calls" - help="File containing paths to signal calls"/> - <param name="data_type" type="select" label="Data Type"> - <option value="MLST" selected="True">MLST</option> - <option value="SNP">SNP</option> - <option value="CNV">CNV</option> - </param> - </inputs> - - <outputs> - <data name="matrix" label="Distance matrix of ${on_string}" format="tabular" from_work_dir="matrix.tsv"/> - </outputs> - - <help> - - </help> - - <citations> - - </citations> -</tool>
--- a/tools/visualization/visualization.xml Fri Nov 16 15:28:27 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -<tool id="visualization" name="PathOGiST - Visualization" version="1.0.0"> - <description>: Visualize distance matrix</description> - <requirements> - <requirement type="package" version="0.0.1">pathogist</requirement> - </requirements> - - <command><![CDATA[ - PATHOGIST vis $distance $sample $pdf - ]]></command> - - <inputs> - <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/> - <param name="sample" type="text" size="30" value="sample" label="Sample Name"/> - <param name="pdf" type="boolean" checked="false" truevalue="--save_pdf vis.pdf" falsevalue="" label="Save PDF"/> - </inputs> - - <outputs> - <data name="diagram" label="Diagram of ${on_string}" format="png" from_work_dir="sample.png"/> - <data name="pdf_output" label="PDF of ${on_string}" format="pdf" from_work_dir="vis.pdf"> - <filter>pdf == True</filter> - </data> - </outputs> - - <help> - - </help> - - <citations> - - </citations> -</tool>