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changeset 4:077f404ae1bb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:29 -0400
parents 4cd116158aef
children
files get_flanks.py get_flanks.xml macros.xml tool_dependencies.xml
diffstat 4 files changed, 82 insertions(+), 67 deletions(-) [+]
line wrap: on
line diff
--- a/get_flanks.py	Wed Nov 11 12:48:31 2015 -0500
+++ b/get_flanks.py	Thu Jun 22 18:41:29 2017 -0400
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
-#Done by: Guru
-
+# Done by: Guru
 """
 Get Flanking regions.
 
@@ -8,8 +7,10 @@
    -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
    -o, --off=N: Offset
 """
+from __future__ import print_function
 
 import sys
+
 from bx.cookbook import doc_optparse
 from galaxy.tools.util.galaxyops import parse_cols_arg
 
@@ -54,12 +55,12 @@
             j += 1
             try:
                 elems = line.split('\t')
-                #if the start and/or end columns are not numbers, skip that line.
+                # if the start and/or end columns are not numbers, skip that line.
                 assert int(elems[start_col_1])
                 assert int(elems[end_col_1])
                 if strand_col_1 != -1:
                     strand = elems[strand_col_1]
-                #if the stand value is not + or -, skip that line.
+                # if the stand value is not + or -, skip that line.
                 assert strand in ['+', '-']
                 if direction == 'Upstream':
                     if strand == '+':
@@ -184,8 +185,9 @@
     if skipped_lines == j:
         stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
     if skipped_lines > 0:
-        print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
-    print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' % ( direction, region, size, offset )
+        print('Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line ))
+    print('Location: %s, Region: %s, Flank-length: %d, Offset: %d ' % ( direction, region, size, offset ))
+
 
 if __name__ == "__main__":
     main()
--- a/get_flanks.xml	Wed Nov 11 12:48:31 2015 -0500
+++ b/get_flanks.xml	Thu Jun 22 18:41:29 2017 -0400
@@ -1,57 +1,62 @@
 <tool id="get_flanks1" name="Get flanks" version="1.0.0">
-  <description>returns flanking region/s for every gene</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">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
-  <inputs>
-    <param format="interval" name="input" type="data" label="Select data"/>
-    <param name="region" type="select" label="Region">
-      <option value="whole" selected="true">Whole feature</option>
-      <option value="start">Around Start</option>
-      <option value="end">Around End</option>
-    </param>
-    <param name="direction" type="select" label="Location of the flanking region/s">
-      <option value="Upstream">Upstream</option>
-      <option value="Downstream">Downstream</option>
-      <option value="Both">Both</option>
-    </param>
-    <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
-    <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
-    
-    
-  </inputs>
-  <outputs>
-    <data format="interval" name="out_file1" metadata_source="input"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="flanks_inp.bed"/>
-      <param name="offset" value="-500"/>
-      <param name="size" value="1000"/>
-      <param name="direction" value="Both"/>
-      <param name="region" value="whole"/>
-      <output name="out_file1" file="flanks_out1.bed"/>
-    </test>
-    <test>
-      <param name="input" value="flanks_inp.bed"/>
-      <param name="offset" value="200"/>
-      <param name="size" value="1000"/>
-      <param name="direction" value="Downstream"/>
-      <param name="region" value="start" />
-      <output name="out_file1" file="flanks_out2.bed"/>
-    </test>
-  </tests>
- <help> 
-
-This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 
+    <description>returns flanking region/s for every gene</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+python '$__tool_directory__/get_flanks.py'
+'$input'
+'$out_file1'
+$size
+$direction
+$region
+-o $offset
+-l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="interval" label="Select data"/>
+        <param name="region" type="select" label="Region">
+            <option value="whole" selected="true">Whole feature</option>
+            <option value="start">Around Start</option>
+            <option value="end">Around End</option>
+        </param>
+        <param name="direction" type="select" label="Location of the flanking region/s">
+            <option value="Upstream">Upstream</option>
+            <option value="Downstream">Downstream</option>
+            <option value="Both">Both</option>
+        </param>
+        <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
+        <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="flanks_inp.bed"/>
+            <param name="offset" value="-500"/>
+            <param name="size" value="1000"/>
+            <param name="direction" value="Both"/>
+            <param name="region" value="whole"/>
+            <output name="out_file1" file="flanks_out1.bed"/>
+        </test>
+        <test>
+            <param name="input" value="flanks_inp.bed"/>
+            <param name="offset" value="200"/>
+            <param name="size" value="1000"/>
+            <param name="direction" value="Downstream"/>
+            <param name="region" value="start" />
+            <output name="out_file1" file="flanks_out2.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
 
 **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
 
 -----
 
-
 **Example 1**
 
 - For the following dataset::
@@ -75,8 +80,5 @@
    chr22  500  800  NM_028946 0 -
 
 .. image:: flanks_ex2.gif
-
-</help>  
-
-
+    ]]></help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:41:29 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/tool_dependencies.xml	Wed Nov 11 12:48:31 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>