| Previous changeset 3:0a3e3133b09d (2015-11-11) Next changeset 5:21898544368b (2022-06-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 |
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modified:
basecoverage.xml gops_basecoverage.py operation_filter.py |
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added:
macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r 0a3e3133b09d -r 2cedec3759e4 basecoverage.xml --- a/basecoverage.xml Wed Nov 11 12:47:11 2015 -0500 +++ b/basecoverage.xml Thu Jun 22 18:40:06 2017 -0400 |
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| @@ -1,49 +1,43 @@ <tool id="gops_basecoverage_1" name="Base Coverage" version="1.0.0"> - <description>of all intervals</description> - <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command> - <requirements> - <requirement type="package" version="0.7.1">bx-python</requirement> - <requirement type="package" version="1.0.0">galaxy-ops</requirement> - </requirements> - <inputs> - <param format="interval" name="input1" type="data"> - <label>Compute coverage for</label> - </param> - </inputs> - <outputs> - <data format="txt" name="output" /> - </outputs> - <code file="operation_filter.py"/> - <tests> - <test> - <param name="input1" value="1.bed" /> - <output name="output" file="gops_basecoverage_out.txt" /> - </test> - <test> - <param name="input1" value="gops_bigint.interval" /> - <output name="output" file="gops_basecoverage_out2.txt" /> - </test> - </tests> - <help> - + <description>of all intervals</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="operation_filter.py"/> + <command><![CDATA[ +python '$__tool_directory__/gops_basecoverage.py' +'$input1' +'$output' +-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} + ]]></command> + <inputs> + <param name="input1" type="data" format="interval" label="Compute coverage for" /> + </inputs> + <outputs> + <data name="output" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bed" /> + <output name="output" file="gops_basecoverage_out.txt" /> + </test> + <test> + <param name="input1" value="gops_bigint.interval" /> + <output name="output" file="gops_basecoverage_out2.txt" /> + </test> + </tests> + <help><![CDATA[ .. class:: infomark **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total. ------ - -**Screencasts!** - -See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). - -.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations +@SCREENCASTS@ **Example** .. image:: gops_baseCoverage.gif - - -</help> + ]]></help> </tool> |
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| diff -r 0a3e3133b09d -r 2cedec3759e4 gops_basecoverage.py --- a/gops_basecoverage.py Wed Nov 11 12:47:11 2015 -0500 +++ b/gops_basecoverage.py Thu Jun 22 18:40:06 2017 -0400 |
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| @@ -5,12 +5,14 @@ usage: %prog in_file out_file -1, --cols1=N,N,N,N: Columns for start, end, strand in first file """ +from __future__ import print_function import fileinput import sys + +from bx.cookbook import doc_optparse from bx.intervals.io import NiceReaderWrapper from bx.intervals.operations.base_coverage import base_coverage -from bx.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped @@ -34,13 +36,14 @@ try: bases = base_coverage(g1) - except ParseError, exc: + except ParseError as exc: fail( "Invalid file format: %s" % str( exc ) ) out_file = open( out_fname, "w" ) out_file.write( "%s\n" % str( bases ) ) out_file.close() if g1.skipped > 0: - print skipped( g1, filedesc="" ) + print(skipped( g1, filedesc="" )) + if __name__ == "__main__": main() |
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| diff -r 0a3e3133b09d -r 2cedec3759e4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 22 18:40:06 2017 -0400 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.7.1">bx-python</requirement> + <requirement type="package" version="1.0.0">galaxy-ops</requirement> + </requirements> + </xml> + <token name="@SCREENCASTS@"> +----- + +**Screencasts!** + +See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). + +.. _Screencasts: https://galaxyproject.org/learn/interval-operations/ + +----- + </token> +</macros> |
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| diff -r 0a3e3133b09d -r 2cedec3759e4 operation_filter.py --- a/operation_filter.py Wed Nov 11 12:47:11 2015 -0500 +++ b/operation_filter.py Thu Jun 22 18:40:06 2017 -0400 |
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| @@ -1,8 +1,7 @@ # runs after the job (and after the default post-filter) +from galaxy.jobs.handler import JOB_ERROR from galaxy.tools.parameters import DataToolParameter -from galaxy.jobs.handler import JOB_ERROR - # Older py compatibility try: set() @@ -14,7 +13,7 @@ dbkeys = set() data_param_names = set() data_params = 0 - for name, param in page_param_map.iteritems(): + for name, param in page_param_map.items(): if isinstance( param, DataToolParameter ): # for each dataset parameter if param_values.get(name, None) is not None: @@ -53,7 +52,6 @@ try: if stderr and len( stderr ) > 0: raise Exception( stderr ) - except Exception: data.blurb = JOB_ERROR data.state = JOB_ERROR |
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| diff -r 0a3e3133b09d -r 2cedec3759e4 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:47:11 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bx-python" version="0.7.1"> - <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="galaxy-ops" version="1.0.0"> - <repository changeset_revision="9cbb20b85c01" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |