Mercurial > repos > peterjc > seq_primer_clip

changeset 5:530c8d6fedd8 draft

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v0.0.15 - internal changes
author peterjc
date Wed, 10 May 2017 13:09:52 -0400
parents 9b074c1db68e
children b9dc7c967ee6
files tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.py tools/seq_primer_clip/seq_primer_clip.xml
diffstat 3 files changed, 19 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/tools/seq_primer_clip/README.rst	Thu Feb 02 11:52:37 2017 -0500
+++ b/tools/seq_primer_clip/README.rst	Wed May 10 13:09:52 2017 -0400
@@ -69,8 +69,10 @@
         - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - Fixed input file help text.
-v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed).
+v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
         - Explicit dependency on ``galaxy_sequence_utils``.
+v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only)
 ======= ======================================================================
 
 
@@ -89,17 +91,17 @@
 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_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    $ planemo shed_update -t testtoolshed --check_diff tools/seq_primer_clip/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    $ planemo shed_update -t toolshed --check_diff tools/seq_primer_clip/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    $ planemo shed_upload --tar_only tools/seq_primer_clip/
     ...
     $ tar -tzf shed_upload.tar.gz 
     test-data/MID4_GLZRM4E04_rnd30.fasta
--- a/tools/seq_primer_clip/seq_primer_clip.py	Thu Feb 02 11:52:37 2017 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Wed May 10 13:09:52 2017 -0400
@@ -29,8 +29,10 @@
 NOTE: Currently it uses Python's regular expression engine for finding the
 primers, which for my needs is fast enough.
 """
+
+import re
 import sys
-import re
+
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
@@ -147,8 +149,8 @@
             # We'll use a set to remove any duplicate patterns
             # if letter not in "NX":
             pattern = seq[:i] + "N" + seq[i + 1:]
-            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                   % (pattern, len(pattern), seq, len(seq))
+            assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
+                                              % (pattern, len(pattern), seq, len(seq)))
             yield make_reg_ex(pattern)
     if mm >= 2:
         for i, letter in enumerate(seq):
@@ -158,8 +160,8 @@
                 # We'll use a set to remove any duplicate patterns
                 # if letter not in "NX":
                 pattern = seq[:i] + "N" + seq[i + 1:i + 1 + k] + "N" + seq[i + k + 2:]
-                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                       % (pattern, len(pattern), seq, len(seq))
+                assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
+                                                  % (pattern, len(pattern), seq, len(seq)))
                 yield make_reg_ex(pattern)
 
 
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Thu Feb 02 11:52:37 2017 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Wed May 10 13:09:52 2017 -0400
@@ -1,18 +1,14 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    <version_command>
+python $__tool_directory__/seq_primer_clip.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>