changeset 3:32e1c8dac438 draft

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

--- a/concat.xml	Wed Nov 11 12:47:51 2015 -0500
+++ b/concat.xml	Thu Jun 22 18:40:46 2017 -0400
@@ -1,53 +1,47 @@
 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
-  <description>two datasets into one 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_concat.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} $sameformat</command>
-  <inputs>
-    <param format="interval" name="input1" type="data" help="First dataset">
-      <label>Concatenate</label>
-    </param>
-    <param format="interval" name="input2" type="data" help="Second dataset">
-      <label>with</label>
-    </param>
-    <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" label="Both datasets are same filetype?" checked="true" help="If unchecked Second dataset will be forced into format of First dataset">
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py"/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2.bed" />
-      <param name="sameformat" value="true" />
-      <output name="output" file="gops_concat_out1.bed" />     
-    </test>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="1.interval" />
-      <param name="sameformat" value="false" />
-      <output name="output" file="gops_concat_out2.bed" />     
-    </test>   
-  </tests>
-  <help>
-
+    <description>two datasets into one dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_concat.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}
+$sameformat
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Concatenate" help="First dataset" />
+        <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
+        <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" checked="true" label="Both datasets are in the same format?" help="If unchecked, Second dataset will be forced into the format of First 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" />
+            <param name="sameformat" value="true" />
+            <output name="output" file="gops_concat_out1.bed" />
+        </test>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="1.interval" />
+            <param name="sameformat" value="false" />
+            <output name="output" file="gops_concat_out2.bed" />
+        </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.
 
------
-
-**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**
 
@@ -58,6 +52,5 @@
 **Example**
 
 .. image:: gops_concatenate.gif
-
-</help>
+    ]]></help>
 </tool>

--- a/gops_concat.py	Wed Nov 11 12:47:51 2015 -0500
+++ b/gops_concat.py	Thu Jun 22 18:40:46 2017 -0400
@@ -12,12 +12,14 @@
     -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file
     -s, --sameformat: All files are precisely the same format.
 """
+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.concat import concat
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -59,16 +61,17 @@
                 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 18:40:46 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 12:47:51 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:40:46 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 12:47:51 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>