Mercurial > repos > pjbriggs > motif_tools

changeset 1:2f34d5e91bc7 draft

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Update to fix README and add some tests.
author pjbriggs
date Wed, 21 Mar 2018 06:34:12 -0400
parents b42da9dc4507
children 96a4ee27b08a
files README.rst Scan_IUPAC_output_each_match.xml Scan_IUPAC_output_matches_per_seq.xml test-data/iupac_each_match.gff test-data/iupac_matches_per_seq.out test-data/phix.fa
diffstat 6 files changed, 112 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Wed Mar 21 05:44:12 2018 -0400
+++ b/README.rst	Wed Mar 21 06:34:12 2018 -0400
@@ -26,7 +26,7 @@
 ===================
 
 To add these to Galaxy put the following lines in tool_conf.xml for each:
-tool that you want:
+tool that you want::
 
     <tool file="motif_tools/Scan_IUPAC_output_each_match.xml" />
     <tool file="motif_tools/Scan_IUPAC_output_matches_per_seq.xml" />
@@ -42,7 +42,7 @@
 ========== =====================================================================
 =
 Version    Changes
----------- ---------------------------------------------------------------------
+---------- ----------------------------------------------------------------------
 - 1.0.1    Updates to use conda dependency resolution and tidy up XML
 - 1.0.0    Initial version
 ========== =====================================================================
--- a/Scan_IUPAC_output_each_match.xml	Wed Mar 21 05:44:12 2018 -0400
+++ b/Scan_IUPAC_output_each_match.xml	Wed Mar 21 06:34:12 2018 -0400
@@ -20,6 +20,15 @@
   <outputs>
     <data format="gff" name="output" />
   </outputs>
+  <tests>
+    <test>
+      <param name="iupac" value="WGATAR" />
+      <param name="fasta" value="phix.fa" />
+      <param name="label" value="IUPAC_or_name" />
+      <param name="strand" value="0" />
+      <output name="output" file="iupac_each_match.gff" />
+    </test>
+  </tests>
 
   <help>
 .. class:: infomark
--- a/Scan_IUPAC_output_matches_per_seq.xml	Wed Mar 21 05:44:12 2018 -0400
+++ b/Scan_IUPAC_output_matches_per_seq.xml	Wed Mar 21 06:34:12 2018 -0400
@@ -19,6 +19,14 @@
   <outputs>
     <data format="tabular" name="output" />
   </outputs>
+  <tests>
+    <test>
+      <param name="iupac" value="WGATAR" />
+      <param name="fasta" value="phix.fa" />
+      <param name="strand" value="0" />
+      <output name="output" file="iupac_matches_per_seq.out" />
+    </test>
+  </tests>
 
   <help>
 .. class:: infomark
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iupac_each_match.gff	Wed Mar 21 06:34:12 2018 -0400
@@ -0,0 +1,14 @@
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	70	75	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	2282	2287	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	2439	2444	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	2526	2531	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	3218	3223	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	3263	3268	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	3833	3838	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	4622	4627	.	+	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	64	69	.	-	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	346	351	.	-	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	2086	2091	.	-	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	3287	3292	.	-	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	3530	3535	.	-	.	IUPAC_or_name
+gi|9626372|ref|NC_001422.1|	RegexSearch	CNS	4718	4723	.	-	.	IUPAC_or_name
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iupac_matches_per_seq.out	Wed Mar 21 06:34:12 2018 -0400
@@ -0,0 +1,1 @@
+gi|9626372|ref|NC_001422.1|	14
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phix.fa	Wed Mar 21 06:34:12 2018 -0400
@@ -0,0 +1,78 @@
+>gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174, complete genome
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA