# HG changeset patch
# User peterjc
# Date 1431528989 14400
# Node ID 91f55ee8fea5f99219e777cd4825cfa1980dae1b
# Parent  1a83f5ab9e95742eb387e2226e1d11c5ad67350b
v0.0.11; more tests and assorting minor changes

diff -r 1a83f5ab9e95 -r 91f55ee8fea5 test-data/k12_hypothetical_alt.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/k12_hypothetical_alt.tabular	Wed May 13 10:56:29 2015 -0400
@@ -0,0 +1,2 @@
+#ID and Description	Length
+gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli str. K-12 substr. MG1655]	98
diff -r 1a83f5ab9e95 -r 91f55ee8fea5 tools/seq_select_by_id/README.rst
--- a/tools/seq_select_by_id/README.rst	Thu Nov 21 04:54:59 2013 -0500
+++ b/tools/seq_select_by_id/README.rst	Wed May 13 10:56:29 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
 ===============================================================
 
-This tool is copyright 2011-2013 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.
 
@@ -36,20 +36,20 @@
 
 There are just two files to install to use this tool from within Galaxy:
 
-* seq_select_by_id.py (the Python script)
-* seq_select_by_id.xml (the Galaxy tool definition)
+* ``seq_select_by_id.py`` (the Python script)
+* ``seq_select_by_id.xml`` (the Galaxy tool definition)
 
-The suggested location is a dedicated tools/seq_select_by_id folder.
+The suggested location is a dedicated ``tools/seq_select_by_id`` folder.
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line::
 
     <tool file="seq_select_by_id/seq_select_by_id.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id seq_select_by_id
+    $ ./run_tests.sh -id seq_select_by_id
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -73,7 +73,18 @@
         - Fixed Biopython dependency setup.
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
-v0.0.8  - Corrected automated dependency definition
+v0.0.8  - Corrected automated dependency definition.
+v0.0.9  - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+        - 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).
+        - Quote filenames in case of spaces (internal change only).
 ======= ======================================================================
 
 
@@ -86,21 +97,31 @@
 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
+    $ 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
 
 
 Licence (MIT)
diff -r 1a83f5ab9e95 -r 91f55ee8fea5 tools/seq_select_by_id/seq_select_by_id.py
--- a/tools/seq_select_by_id/seq_select_by_id.py	Thu Nov 21 04:54:59 2013 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.py	Wed May 13 10:56:29 2015 -0400
@@ -19,34 +19,32 @@
 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
 All rights reserved. See accompanying text file for licence details (MIT
 license).
-
-This is version 0.0.6 of the script.
 """
 import sys
 
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(err)
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.6"
+    print "v0.0.9"
     sys.exit(0)
 
 #Parse Command Line
 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"):
@@ -56,22 +54,35 @@
     #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):
-    """Read tabular file and record all specified identifiers."""
+    """Read tabular file and record all specified identifiers.
+
+    Will print a single warning to stderr if any of the fields have
+    non-trailing white space (only the first word will be used as
+    the identifier).
+    """
     handle = open(tabular_file, "rU")
+    warn = False
     for line in handle:
         if line.strip() and not line.startswith("#"):
-            yield line.rstrip("\n").split("\t")[col].strip()
+            field = line.rstrip("\n").split("\t")[col].strip()
+            parts = field.split(None, 1)
+            if len(parts) > 1 and not warn:
+                warn = "WARNING: Some of your identifiers had white space in them, " + \
+                       "using first word only. e.g.:\n%s\n" % field
+            yield parts[0]
     handle.close()
+    if warn:
+        sys.stderr.write(warn)
 
 #Index the sequence file.
 #If very big, could use SeqIO.index_db() to avoid memory bottleneck...
@@ -83,7 +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
@@ -109,7 +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()
@@ -123,7 +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()
 
diff -r 1a83f5ab9e95 -r 91f55ee8fea5 tools/seq_select_by_id/seq_select_by_id.xml
--- a/tools/seq_select_by_id/seq_select_by_id.xml	Thu Nov 21 04:54:59 2013 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Wed May 13 10:56:29 2015 -0400
@@ -1,35 +1,25 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
+<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="fasta" label="Selected sequences">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/>
     </outputs>
     <tests>
         <test>
@@ -37,6 +27,35 @@
             <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>
+            <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" />
+            <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>
@@ -69,4 +88,8 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>
diff -r 1a83f5ab9e95 -r 91f55ee8fea5 tools/seq_select_by_id/tool_dependencies.xml
--- a/tools/seq_select_by_id/tool_dependencies.xml	Thu Nov 21 04:54:59 2013 -0500
+++ b/tools/seq_select_by_id/tool_dependencies.xml	Wed May 13 10:56:29 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.62">
-        <repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>