Mercurial > repos > peterjc > sample_seqs

changeset 4:d3aa9f25c24c draft

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v0.2.2 use format_source and other internal changes
author peterjc
date Wed, 05 Aug 2015 12:30:18 -0400
parents 02c13ef1a669
children 6b71ad5d43fb
files tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.xml
diffstat 2 files changed, 42 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/tools/sample_seqs/README.rst	Fri Mar 27 09:34:27 2015 -0400
+++ b/tools/sample_seqs/README.rst	Wed Aug 05 12:30:18 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to sub-sample sequence files
 ========================================
 
-This tool is copyright 2014-2014 by Peter Cock, The James Hutton Institute
+This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -56,7 +56,7 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial version.
-v0.1.1  - Using optparse to provide a proper command line API.
+v0.1.1  - Using ``optparse`` to provide a proper Python command line API.
 v0.1.2  - Interleaved mode for working with paired records.
         - Tool definition now embeds citation information.
 v0.2.0  - Option to give number of sequences (or pairs) desired.
@@ -66,6 +66,9 @@
 v0.2.1  - Was missing a file for the functional tests.
         - Included testing of stdout messages.
         - Includes testing of failure modes.
+v0.2.2  - Reorder XML elements (internal change only).
+        - Use ``format_source=...``` tag.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -75,32 +78,41 @@
 This script and related tools are being developed on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
 
-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_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/
+    ...
+
+or::
+
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/
+    ...
+
+To just build and check the tar ball, use::
 
-    $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/ecoli.pair_sample_N100.fastq test-data/ecoli.sample_C10.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
-
-Check this worked::
-
-    $ tar -tzf sample_seqs.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/sample_seqs/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
+    test-data/ecoli.fastq
+    test-data/ecoli.pair_sample_N100.fastq
+    test-data/ecoli.sample_C10.fastq
+    test-data/ecoli.sample_N100.fastq
+    test-data/get_orf_input.Suis_ORF.prot.fasta
+    test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta
+    test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta
+    test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta
+    test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
     tools/sample_seqs/README.rst
     tools/sample_seqs/sample_seqs.py
     tools/sample_seqs/sample_seqs.xml
     tools/sample_seqs/tool_dependencies.xml
-    test-data/ecoli.fastq
-    test-data/ecoli.sample_N100.fastq
-    test-data/ecoli.pair_sample_N100.fastq
-    test-data/ecoli.sample_C10.fastq
-    test-data/get_orf_input.Suis_ORF.prot.fasta
-    test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
-    test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta
-    test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta
-    test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta
-    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
-    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
-    test-data/MID4_GLZRM4E04_rnd30_pair_sample.sff
-    test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
-    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
 
 
 Licence (MIT)
--- a/tools/sample_seqs/sample_seqs.xml	Fri Mar 27 09:34:27 2015 -0400
+++ b/tools/sample_seqs/sample_seqs.xml	Wed Aug 05 12:30:18 2015 -0400
@@ -1,9 +1,14 @@
-<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.1">
+<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.2">
     <description>e.g. to reduce coverage</description>
     <requirements>
         <requirement type="package" version="1.65">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">sample_seqs.py --version</version_command>
     <command interpreter="python">
 sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file"
@@ -18,11 +23,6 @@
 --interleaved
 #end if
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file" help="FASTA, FASTQ, or SFF format." />
         <conditional name="sampling">
@@ -45,7 +45,7 @@
         <param name="interleaved" type="boolean" label="Interleaved paired reads" help="This mode keeps paired reads together (e.g. take every 5th read pair)" />
     </inputs>
     <outputs>
-        <data name="output_file" format="input" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/>
     </outputs>
     <tests>
         <test>