changeset 16:9aa51c1a17cc draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/seq_select_by_id commit 3abdffd9ade48aa2c2b5f52572d0f77b4f3d2c9c

--- a/tools/seq_select_by_id/README.rst	Thu Nov 27 06:38:33 2014 -0500
+++ b/tools/seq_select_by_id/README.rst	Wed May 13 10:53:36 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
 ===============================================================
 
-This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -79,6 +79,11 @@
         - Include input dataset name in output dataset names.
         - If white space is found in the requested tabular field then only
           the first word is used as the identifier (with a warning to stderr).
+v0.0.10 - Includes testing of stdout messages.
+        - Includes testing of failure modes.
+v0.0.11 - Use the ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -91,22 +96,31 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
+
+or::
 
-    $ tar -czf seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular test-data/k12_hypothetical_alt.tabular
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf seq_select_by_id.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/k12_hypothetical.fasta
+    test-data/k12_hypothetical.tabular
+    test-data/k12_hypothetical_alt.tabular
+    test-data/k12_ten_proteins.fasta
     tools/seq_select_by_id/README.rst
     tools/seq_select_by_id/seq_select_by_id.py
     tools/seq_select_by_id/seq_select_by_id.xml
     tools/seq_select_by_id/tool_dependencies.xml
-    test-data/k12_ten_proteins.fasta
-    test-data/k12_hypothetical.fasta
-    test-data/k12_hypothetical.tabular
-    test-data/k12_hypothetical_alt.tabular
 
 
 Licence (MIT)

--- a/tools/seq_select_by_id/seq_select_by_id.py	Thu Nov 27 06:38:33 2014 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.py	Wed May 13 10:53:36 2015 -0400
@@ -22,7 +22,7 @@
 """
 import sys
 
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(err)
 
@@ -34,17 +34,17 @@
 try:
     tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:]
 except ValueError:
-    stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+    sys_exit("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
 try:
     if col_arg.startswith("c"):
         column = int(col_arg[1:])-1
     else:
         column = int(col_arg)-1
 except ValueError:
-    stop_err("Expected column number, got %s" % col_arg)
+    sys_exit("Expected column number, got %s" % col_arg)
 
 if seq_format == "fastqcssanger":
-    stop_err("Colorspace FASTQ not supported.")
+    sys_exit("Colorspace FASTQ not supported.")
 elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]:
     seq_format = seq_format.lower()
 elif seq_format.lower().startswith("fastq"):
@@ -54,13 +54,13 @@
     #We don't care what the scores are
     seq_format = "qual"
 else:
-    stop_err("Unrecognised file format %r" % seq_format)
+    sys_exit("Unrecognised file format %r" % seq_format)
 
 
 try:
     from Bio import SeqIO
 except ImportError:
-    stop_err("Biopython 1.54 or later is required")
+    sys_exit("Biopython 1.54 or later is required")
 
 
 def parse_ids(tabular_file, col):
@@ -94,7 +94,7 @@
     try:
         from Bio.SeqIO.SffIO import SffIterator, SffWriter
     except ImportError:
-        stop_err("Requires Biopython 1.54 or later")
+        sys_exit("Requires Biopython 1.54 or later")
 
     try:
         from Bio.SeqIO.SffIO import ReadRocheXmlManifest
@@ -120,7 +120,7 @@
     except KeyError, err:
         out_handle.close()
         if name not in records:
-            stop_err("Identifier %r not found in sequence file" % name)
+            sys_exit("Identifier %r not found in sequence file" % name)
         else:
             raise err
     out_handle.close()
@@ -134,7 +134,7 @@
             out_handle.write(records.get_raw(name))
         except KeyError:
             out_handle.close()
-            stop_err("Identifier %r not found in sequence file" % name)
+            sys_exit("Identifier %r not found in sequence file" % name)
         count += 1
     out_handle.close()
 

--- a/tools/seq_select_by_id/seq_select_by_id.xml	Thu Nov 27 06:38:33 2014 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Wed May 13 10:53:36 2015 -0400
@@ -1,25 +1,25 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.9">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">seq_select_by_id.py --version</version_command>
-    <command interpreter="python">
-seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">seq_select_by_id.py --version</version_command>
+    <command interpreter="python">
+seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
+    </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
         <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
         <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="input" metadata_source="input_file" label="Selected sequences from $input_file.name"/>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/>
     </outputs>
     <tests>
         <test>
@@ -27,6 +27,10 @@
             <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
             <param name="column" value="1" />
             <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
+            <assert_stdout>
+                <has_line line="Indexed 10 sequences" />
+                <has_line line="Selected 1 sequences by ID" />
+            </assert_stdout>
         </test>
         <!-- this version has white space in the identifier column (id and description) -->
         <test>
@@ -34,6 +38,24 @@
             <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" />
             <param name="column" value="1" />
             <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
+            <assert_stdout>
+                <has_line line="Indexed 10 sequences" />
+                <has_line line="Selected 1 sequences by ID" />
+            </assert_stdout>
+            <assert_stderr>
+                <has_line line="WARNING: Some of your identifiers had white space in them, using first word only. e.g.:" />
+            </assert_stderr>
+        </test>
+        <test expect_failure="true" expect_exit_code="1">
+            <param name="input_file" value="empty.fasta" ftype="fasta" />
+            <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
+            <param name="column" value="1" />
+            <assert_stdout>
+                <has_line line="Indexed 0 sequences" />
+            </assert_stdout>
+            <assert_stderr>
+                <has_line line="Identifier 'gi|16127999|ref|NP_414546.1|' not found in sequence file" />
+            </assert_stderr>
         </test>
     </tests>
     <help>