diff tools/sample_seqs/README.rst @ 2:da64f6a9e32b draft

Uploaded v0.2.0, adds desired count mode

--- a/tools/sample_seqs/README.rst	Thu Mar 27 12:13:22 2014 -0400
+++ b/tools/sample_seqs/README.rst	Fri Mar 06 11:48:09 2015 -0500
@@ -39,11 +39,12 @@
 
     <tool file="sample_seqs/sample_seqs.xml" />
 
-You will also need to install Biopython 1.62 or later. If you want to run
-the unit tests, include this line in ``tools_conf.xml.sample`` and the sample
-FASTA files under the ``test-data`` directory. Then::
+You will also need to install Biopython 1.62 or later.
 
-    ./run_functional_tests.sh -id sample_seqs
+If you wish to run the unit tests, also	move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    ./run_tests.sh -id sample_seqs
 
 That's it.
 
@@ -55,6 +56,13 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial version.
+v0.1.1  - Using optparse to provide a proper 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.
+          This works by first counting all your sequences, then calculates
+          the percentage required in order to sample them uniformly (evenly).
+          This makes two passes through the input and is therefore slower. 
 ======= ======================================================================
 
 
@@ -67,7 +75,7 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ 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/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
+    $ 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::
 
@@ -78,10 +86,18 @@
     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)