| Previous changeset 0:217aedbdd0d0 (2012-03-13) |
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Commit message:
Add tool_dependencies.xml and test case |
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modified:
fastq-mcf.xml |
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added:
README test-data/adapters.fa test-data/test_mcf_mates.fq test-data/test_mcf_reads.fq test-data/testout_mcf_mates.fq test-data/testout_mcf_reads.fq tool_dependencies.xml |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,19 @@ + +== ea-utils Galaxy Wrapper == + +This is a Galaxy wrapper for some ea-utils tools, fastq-join and sam-stats. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies. + +Otherwise, make sure fastq-join and sam-stats are in the path. +Move the test data files to your galaxy root test-data. +Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them. +Restart the Galaxy server. + +** Attribution ** + +The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/ + + |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f fastq-mcf.xml --- a/fastq-mcf.xml Tue Mar 13 14:44:46 2012 -0400 +++ b/fastq-mcf.xml Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="fastq_mcf" name="FastqMcf" version="1.0"> <description>sequence quality filtering and clipping</description> <requirements> - <requirement type="binary">fastq-mcf</requirement> + <requirement type="package" version="1.1.2-484">ea-utils</requirement> </requirements> <version_string>fastq-mcf -V</version_string> <command>fastq-mcf @@ -41,7 +41,9 @@ #if len($trimming.sampcnt.__str__) > 0 -s $trimming.sampcnt #end if - $trimming.ilv3 + #if len($trimming.ilv3.__str__.strip()) > 0 + -$trimming.ilv3 + #end if $trimming.rmns #end if #if $noclip == True : @@ -120,9 +122,9 @@ </param> <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/> <param name="ilv3" type="select" label="illumina PF filtering"> - <option value=" ">Default</option> - <option value="-U">Disable illumina PF filtering</option> - <option value="-u">Enable illumina PF filtering</option> + <option value="">Default</option> + <option value="U">Disable illumina PF filtering</option> + <option value="u">Enable illumina PF filtering</option> </param> </when> </conditional> @@ -143,7 +145,24 @@ <filter>(noclip == False and mates != None)</filter> </data> </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <tests> + <test> + <param name="adpaters" ftype="fasta" value="adapters.fa" /> + <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" /> + <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" /> + <param name="choice" value="user_set" /> + <param name="nkeep" value="16" /> + <param name="qthr" value="15" /> + <param name="qwin" value="5" /> + <param name="pctns" value="10" /> + <param name="ilv3" value="u" /> + <param name="phred" value="33" /> + <output name="reads_out" file="testout_mcf_reads.fq" /> + <output name="mates_out" file="testout_mcf_mates.fq" /> + </test> </tests> <help> **What it does** @@ -156,6 +175,8 @@ Detect N's, and remove from ends Remove reads with CASAVA 'Y' flag (purity filtering) Discard sequences that are too short after all of the above + + Keep multiple mate-reads in sync while doing all of the above .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/adapters.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adapters.fa Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,2 @@ +>Trufseq_Universal_Adaptor +AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/test_mcf_mates.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_mcf_mates.fq Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,20 @@ +@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 2:N:0:CGATGT +CTGGATTTGAAATCTTTAGCGGAGCGGGAACGCCGGCGCGGAAGGGTCTCTACACAGGGCCCGGTCCGCCCTTGCGCTCTCCTTAATGNNNNNNNNNNCGC ++ +@CCF?EFFHHHGHHHIFGI@HGGIEHIGIJGI6@@E>B8>??:DBD++399>ACCDDDD@DBDD58@BBDDDDD@@<@BDDDDC>CDC############# +@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 2:N:0:CGATGT +CCCGGGGCCTCCCATTAAGGTCGCACTTGGACCCATTGCCATAGGTCTGGCTGTGGTAGCGTTTAAGACGATGCTGCTTGGAGGCCTTGGCTGTTTCATCA ++ +BCCFFFFDHFFHGIHIHGJJIJJGGIIJJJIDHGJIJEIIIIIJJIIJIJHHHEEF;>DDA>BBB@CAABBBDDCDDDDDDAD@@?CDDDCCB?ACCDDC# +@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 2:N:0:CGATGT +GTTACTCAGCATTTATTCATGCCTGCTGTGTACGGAAAGGGCAGTTACAAAGGAAAGCCTTGATGATTCTGCTTCCAAGAAACGTGAAGATCAGATAATAT ++ +CBCFFFFFHHHHHJIJJIIJJJJJIIJIHIHIJJJIJIJIJJIIIIIIJJGGIIJJJIJJJJHIJJJJHIJHGHHHHFFFFFEDECBDDDDDCCDDDCDEE +@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 2:N:0:CGATGT +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAACAGAAAAAGAAAGAAGGAAAGGNGAGT ++ +CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?#################################### +@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 2:N:0:ACAGTG +GGATCGGGAAAGGGGGGGGGGGGGGAAAAGGGGGGATTTCCGGGGGGGCCGGTTCTTTTAAAAAAAAAAAAAAAGAAAACAGAAACAGAAGATGGACAACA ++ +CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?#################################### |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/test_mcf_reads.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_mcf_reads.fq Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,20 @@ +@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 1:N:0:CGATGT +CTGGTATTGTCTCTTCCCACACTGAACTCTGGGGAATTCGATGTGTGGCACAGCCCGGCTCAGCCTGCCCGCTGGTGGGAGCCCCTGGGAAGCTGCGGCGC ++ +@@CFDDFFGH>CAEH:CGHIJJJJEIHJJHIJJJ?DHIDIJHGEGHJG;FHC9@B(5@6A=EH:B@B@2=>>B?BDCBD<B52<<ABD?<?B1@A9>B### +@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 1:N:0:CGATGT +GGCAGAGCCAATCTTCGGACGTGGTGATTGTCTCCTCTAAGTACAAACAGCGCTATGAGTGTCGCCTGCCAGCTGGAGCTATTCACTTCCAGCGTGAAAGG ++ +BC@FFFFFHHHGFHIIJJIJGFHICFCGIHGFHFGGCHD@F?B?BGGHJJIG6D@EHEHHEHCD259?AACD@AC59?,(5>A,;>:@C(::(029?8>@A +@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 1:N:0:CGATGT +GTACACTTGAACACATTTTTCTAACCTTAGAAAATACCTACAAGGCCTGTTGTCTTGACCCATTACTCAATTGTCCCTGGCATATTATCTGATCTTCACGT ++ +CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJGIIJGGGDHHHIHIHHEIJIJJIIGGIIIIFEHHHHFEFFFDEEEDCEEEDEDC?A +@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 1:N:0:CGATGT +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAAAAAAAACAAGCGACAAGGACAGA ++ +CCCFFFFFHHHHHJJJJJIJJJJJJJJJIJGHFFHIAHIFGGIIJJIJJFIJIHJIHHHGEGFE>CFFEB############################### +@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 1:N:0:ACAGTG +GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAACAACAGAAAAAACAAAGCGCGAACAGTGC ++ +CCCFFFFFHHHHHJIJJIJIJHJJJJJJJHIGIGIHJFHFFDIIJGIIIJJJHHFIJJJJJJHCEHHFD################################ |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/testout_mcf_mates.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout_mcf_mates.fq Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,20 @@ +@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 2:N:0:CGATGT +CTGGATTTGAAATCTTTAGCGGAGCGGGAACGCCGGCGCGGAAGGGTCTCTACACAGGGCCCGGTCCGCCCTTGCGCTCTCCTTAATG ++ +@CCF?EFFHHHGHHHIFGI@HGGIEHIGIJGI6@@E>B8>??:DBD++399>ACCDDDD@DBDD58@BBDDDDD@@<@BDDDDC>CDC +@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 2:N:0:CGATGT +CCCGGGGCCTCCCATTAAGGTCGCACTTGGACCCATTGCCATAGGTCTGGCTGTGGTAGCGTTTAAGACGATGCTGCTTGGAGGCCTTGGCTGTTTCATC ++ +BCCFFFFDHFFHGIHIHGJJIJJGGIIJJJIDHGJIJEIIIIIJJIIJIJHHHEEF;>DDA>BBB@CAABBBDDCDDDDDDAD@@?CDDDCCB?ACCDDC +@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 2:N:0:CGATGT +GTTACTCAGCATTTATTCATGCCTGCTGTGTACGGAAAGGGCAGTTACAAAGGAAAGCCTTGATGATTCTGCTTCCAAGAAACGTGAAGATCAGATAATAT ++ +CBCFFFFFHHHHHJIJJIIJJJJJIIJIHIHIJJJIJIJIJJIIIIIIJJGGIIJJJIJJJJHIJJJJHIJHGHHHHFFFFFEDECBDDDDDCCDDDCDEE +@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 2:N:0:CGATGT +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAA ++ +CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD? +@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 2:N:0:ACAGTG +GGATCGGGAAAGGGGGGGGGGGGGGAAAAGGGGGGATTTCCGGGGGGGCCGGTTCTTTTAAAAAA ++ +CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD? |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/testout_mcf_reads.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout_mcf_reads.fq Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,20 @@ +@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 1:N:0:CGATGT +CTGGTATTGTCTCTTCCCACACTGAACTCTGGGGAATTCGATGTGTGGCACAGCCCGGCTCAGCCTGCCCGCTGGTGGGAGCCCCTGGGAAGCTGCGG ++ +@@CFDDFFGH>CAEH:CGHIJJJJEIHJJHIJJJ?DHIDIJHGEGHJG;FHC9@B(5@6A=EH:B@B@2=>>B?BDCBD<B52<<ABD?<?B1@A9>B +@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 1:N:0:CGATGT +GGCAGAGCCAATCTTCGGACGTGGTGATTGTCTCCTCTAAGTACAAACAGCGCTATGAGTGTCGCCTGCCAGCTGGAGCTATTCACTTCCAGCGTGAAAGG ++ +BC@FFFFFHHHGFHIIJJIJGFHICFCGIHGFHFGGCHD@F?B?BGGHJJIG6D@EHEHHEHCD259?AACD@AC59?,(5>A,;>:@C(::(029?8>@A +@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 1:N:0:CGATGT +GTACACTTGAACACATTTTTCTAACCTTAGAAAATACCTACAAGGCCTGTTGTCTTGACCCATTACTCAATTGTCCCTGGCATATTATCTGATCTTCACGT ++ +CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJGIIJGGGDHHHIHIHHEIJIJJIIGGIIIIFEHHHHFEFFFDEEEDCEEEDEDC?A +@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 1:N:0:CGATGT +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAA ++ +CCCFFFFFHHHHHJJJJJIJJJJJJJJJIJGHFFHIAHIFGGIIJJIJJFIJIHJIHHHGEGFE>CFFEB +@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 1:N:0:ACAGTG +GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAA ++ +CCCFFFFFHHHHHJIJJIJIJHJJJJJJJHIGIGIHJFHFFDIIJGIIIJJJHHFIJJJJJJHCEHHFD |
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| diff -r 217aedbdd0d0 -r b61f1466ce8f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Apr 01 10:28:17 2013 -0500 |
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| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ea-utils" version="1.1.2-484"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://ea-utils.googlecode.com/files/ea-utils.1.1.2-484.tar.gz</action> + <!-- Unable to get varcall to compile properly we don't need it, so skip --> + <action type="shell_command">sed -i.bak 's/varcall$//' Makefile</action> + <action type="shell_command">PREFIX=$INSTALL_DIR make install</action> + <!-- For some reason, this is not installed by the Makefile, so move it ourselves --> + <action type="move_file"> + <source>sam-stats</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency> |