[hg] galaxy 2856: Modified test data and tool conf for fastq stats - galaxy-dev

9 Oct 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/4d5b24d03226
changeset: 2856:4d5b24d03226
user:      Anton Nekrutenko anton@bx.psu.edu
date:      Thu Oct 08 14:50:28 2009 -0400
description:
Modified test data and tool conf for fastq stats
3 file(s) affected in this change:
test-data/fastq_stats1.fastq
tools/fastx_toolkit/fastx_quality_statistics.xml
tools/metag_tools/split_paired_reads.xml
diffs (85 lines):
diff -r d5a77c9e869e -r 4d5b24d03226 test-data/fastq_stats1.fastq

--- a/test-data/fastq_stats1.fastq	Thu Oct 08 14:09:52 2009 -0400
+++ b/test-data/fastq_stats1.fastq	Thu Oct 08 14:50:28 2009 -0400
@@ -1,36 +1,36 @@
 @CSHL_3_FC042AGLLWW:1:2:7:203
 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
 +CSHL_3_FC042AGLLWW:1:2:7:203
-aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+BBC?7?B6>ABB?B;BBBCC9&;BCBBBBBBBB>>A
 @CSHL_3_FC042AGLLWW:1:2:7:33
 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
 +CSHL_3_FC042AGLLWW:1:2:7:33
-Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+8BBB?B;BB8?6@9B8BB=8.&1?,&;931&&&(BB
 @CSHL_3_FC042AGLLWW:1:2:7:169
 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
 +CSHL_3_FC042AGLLWW:1:2:7:169
-a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+B@.?B=6BBB@.@BBBBBBBBBBBBBBB7=;6(663
 @CSHL_3_FC042AGLLWW:1:2:7:1436
 AATTATTTATTAAATTTTAATAATATGGGAGACACT
 +CSHL_3_FC042AGLLWW:1:2:7:1436
-a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+B?BBBBBBBBBBBBBBB@6ABBBBB@4@BBBBB77<
 @CSHL_3_FC042AGLLWW:1:2:7:292
 GGAGAAATACACACAATTGGTTAATCCCCCTATATA
 +CSHL_3_FC042AGLLWW:1:2:7:292
-babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+CBCBBBBBBB6.BBBBBBBBBBB=9&66&1@>6&3&
 @CSHL_3_FC042AGLLWW:1:2:7:1819
 AATTCAAACCACCCCAACCCACACACAGAGATACAA
 +CSHL_3_FC042AGLLWW:1:2:7:1819
-a\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+B==2777-BB-0&96866&,66-&.6&66,6-*2.6
 @CSHL_3_FC042AGLLWW:1:2:7:1875
 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
 +CSHL_3_FC042AGLLWW:1:2:7:1875
-aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+BBBBBBBBB9699&9BBBBBA@;BBBBBBBBB9&96
 @CSHL_3_FC042AGLLWW:1:2:8:624
 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
 +CSHL_3_FC042AGLLWW:1:2:8:624
-aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+BB<4?A9ABB@>>009.6?@<.6@BBBBBBBBBBBB
 @CSHL_3_FC042AGLLWW:1:2:8:250
 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
 +CSHL_3_FC042AGLLWW:1:2:8:250
-aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
+BBBBBBBB?BBBBBBCCC<,91&6<39;?+6,3,9&
diff -r d5a77c9e869e -r 4d5b24d03226 tools/fastx_toolkit/fastx_quality_statistics.xml
--- a/tools/fastx_toolkit/fastx_quality_statistics.xml	Thu Oct 08 14:09:52 2009 -0400
+++ b/tools/fastx_toolkit/fastx_quality_statistics.xml	Thu Oct 08 14:50:28 2009 -0400
@@ -1,16 +1,14 @@
 <tool id="cshl_fastx_quality_statistics" name="Compute quality statistics">
    <description></description>
-	<command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command>
+	<command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
<inputs>
    	<param format="fastqsanger" name="input" type="data" label="Library to analyse" />
-		<param name="offset" type="hidden" value="33"/>
    </inputs>
<tests>
    	<test>
-			<param name="input" value="fastq_stats1.fastq" ftype="fastq"/>
-			<param name="offset" value="64" />
+			<param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
    		<output name="output" file="fastq_stats1.out" />
    	</test>
    </tests>
diff -r d5a77c9e869e -r 4d5b24d03226 tools/metag_tools/split_paired_reads.xml
--- a/tools/metag_tools/split_paired_reads.xml	Thu Oct 08 14:09:52 2009 -0400
+++ b/tools/metag_tools/split_paired_reads.xml	Thu Oct 08 14:50:28 2009 -0400
@@ -7,8 +7,8 @@
         <param name="input" type="data" format="fastqsanger" label="Your paired-end file" />
     </inputs>
     <outputs>
-        <data name="output1" format="input"/>
-        <data name="output2" format="input"/>
+        <data name="output1" format="fastqsanger"/>
+        <data name="output2" format="fastqsanger"/>
     </outputs>
     <tests>
         <test>

    