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>