changeset 5:1377a23bc02a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

--- a/complement.xml	Fri Dec 18 19:37:08 2015 -0500
+++ b/complement.xml	Thu Jun 22 18:38:23 2017 -0400
@@ -1,55 +1,50 @@
 <tool id="gops_complement_1" name="Complement" version="1.0.0">
-  <description>intervals of a dataset</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_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
-  <inputs>
-    <param format="interval" name="input1" type="data">
-      <label>Complement regions of</label>
-    </param>
-    <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py"/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out.bed" />
-    </test>
-    <test>
-      <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out_diffCols.dat" />
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out2.bed" />
-    </test>
-  </tests>
-  <help>
-
+    <description>intervals of a dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_complement.py'
+'$input1'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+-l '${chromInfo}'
+$allchroms
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Complement regions of" />
+        <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_out.bed" />
+        </test>
+        <test>
+            <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_out_diffCols.dat" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_out2.bed" />
+        </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 complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input 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@
 
 **Syntax**
 
@@ -60,6 +55,5 @@
 **Example**
 
 .. image:: gops_complement.gif
-
-</help>
+    ]]></help>
 </tool>

--- a/gops_complement.py	Fri Dec 18 19:37:08 2015 -0500
+++ b/gops_complement.py	Thu Jun 22 18:38:23 2017 -0400
@@ -7,13 +7,15 @@
     -l, --lengths=N: Filename of .len file for species (chromosome lengths)
     -a, --all: Complement all chromosomes (Genome-wide complement)
 """
+from __future__ import print_function
 
+import fileinput
 import sys
-import fileinput
+
+from bx.cookbook import doc_optparse
 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper
 from bx.intervals.operations.complement import complement
 from bx.intervals.operations.subtract import subtract
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -83,14 +85,15 @@
                 out_file.write( "%s\n" % "\t".join( interval ) )
             else:
                 out_file.write( "%s\n" % interval )
-    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="" )
+        print(skipped( g1, filedesc="" ))
+
 
 if __name__ == "__main__":
     main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:38:23 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	Fri Dec 18 19:37:08 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:38:23 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	Fri Dec 18 19:37:08 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="35e2457234ef" name="package_bx_python_0_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="galaxy-ops" version="1.0.0">
-      <repository changeset_revision="60c9a7af1345" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>