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changeset 4:2cedec3759e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:40:06 -0400
parents 0a3e3133b09d
children 21898544368b
files basecoverage.xml gops_basecoverage.py macros.xml operation_filter.py tool_dependencies.xml
diffstat 5 files changed, 59 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/basecoverage.xml	Wed Nov 11 12:47:11 2015 -0500
+++ b/basecoverage.xml	Thu Jun 22 18:40:06 2017 -0400
@@ -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>
--- a/gops_basecoverage.py	Wed Nov 11 12:47:11 2015 -0500
+++ b/gops_basecoverage.py	Thu Jun 22 18:40:06 2017 -0400
@@ -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()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:40:06 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 12:47:11 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:40:06 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 12:47:11 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>