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changeset 3:4ef9819dc7fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:02 -0400
parents bc9c66c1e9c9
children e3363e087468
files coverage.xml gops_coverage.py macros.xml operation_filter.py tool_dependencies.xml
diffstat 5 files changed, 72 insertions(+), 67 deletions(-) [+]
line wrap: on
line diff
--- a/coverage.xml	Wed Nov 11 12:48:05 2015 -0500
+++ b/coverage.xml	Thu Jun 22 18:41:02 2017 -0400
@@ -1,60 +1,53 @@
 <tool id="gops_coverage_1" name="Coverage" version="1.0.0">
-  <description>of a set of intervals on second set of intervals</description>
-  <requirements>
-    <requirement type="package" version="0.7.1">bx-python</requirement>
-    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
-  </requirements>
-  <command interpreter="python">gops_coverage.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
-  <inputs>
-    <param format="interval" name="input1" type="data" help="First dataset">
-      <label>What portion of</label>
-    </param>
-    <param format="interval" name="input2" type="data" help="Second dataset">
-      <label>is covered by</label>
-    </param>
-   </inputs>
-  <outputs>
-    <data format="interval" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py"/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2.bed" />
-      <output name="output" file="gops_coverage_out.interval" />
-    </test>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2_mod.bed" ftype="interval"/>
-      <output name="output" file="gops_coverage_out_diffCols.interval" />
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" />
-      <param name="input2" value="gops_bigint2.interval" />
-      <output name="output" file="gops_coverage_out2.interval" />
-    </test>
-  </tests>
-  <help>
-
+    <description>of a set of intervals on second set of intervals</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_coverage.py'
+'$input1'
+'$input2'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+-2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="What portion of" help="First dataset" />
+        <param name="input2" type="data" format="interval" label="Is covered by" help="Second dataset" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="2.bed" />
+        <output name="output" file="gops_coverage_out.interval" />
+        </test>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="2_mod.bed" ftype="interval"/>
+            <output name="output" file="gops_coverage_out_diffCols.interval" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" />
+            <param name="input2" value="gops_bigint2.interval" />
+            <output name="output" file="gops_coverage_out2.interval" />
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: infomark
 
 **TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
 
 Find the coverage of intervals in the first dataset on intervals in the second dataset.  The coverage is added as two columns, the first being bases covered, and the second being the fraction of bases covered by that interval.
 
------
-
-**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**
 
-
     if **First dataset** are genes ::
 
       chr11 5203271 5204877 NM_000518 0 -
@@ -90,6 +83,5 @@
       chr11 5203271 5204877 NM_000518 0 - 172   0.107098
 
    implies that 172 nucleotides accounting for 10.7% of the this interval (chr11:5203271-5204877) overlap with repetitive elements.
-
-</help>
-</tool>
\ No newline at end of file
+    ]]></help>
+</tool>
--- a/gops_coverage.py	Wed Nov 11 12:48:05 2015 -0500
+++ b/gops_coverage.py	Thu Jun 22 18:41:02 2017 -0400
@@ -7,11 +7,14 @@
     -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
     -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
 """
+from __future__ import print_function
+
 import fileinput
 import sys
+
+from bx.cookbook import doc_optparse
 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
 from bx.intervals.operations.coverage import coverage
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -48,16 +51,17 @@
                 out_file.write( "%s\n" % "\t".join( line.fields ) )
             else:
                 out_file.write( "%s\n" % line )
-    except ParseError, exc:
+    except ParseError as exc:
         out_file.close()
         fail( "Invalid file format: %s" % str( exc ) )
 
     out_file.close()
 
     if g1.skipped > 0:
-        print skipped( g1, filedesc=" of 1st dataset" )
+        print(skipped( g1, filedesc=" of 1st dataset" ))
     if g2.skipped > 0:
-        print skipped( g2, filedesc=" of 2nd dataset" )
+        print(skipped( g2, filedesc=" of 2nd dataset" ))
+
 
 if __name__ == "__main__":
     main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:41:02 2017 -0400
@@ -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>
--- a/operation_filter.py	Wed Nov 11 12:48:05 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:41:02 2017 -0400
@@ -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
--- a/tool_dependencies.xml	Wed Nov 11 12:48:05 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>