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changeset 0:e6f1c31279db draft

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Initial version with fastq-join
author Lance Parsons <lparsons@princeton.edu>
date Thu, 20 Sep 2012 18:59:38 -0400
parents
children cf4b5125a835
files fastq-join.xml test-data/test_read1.fastq test-data/test_read3.fastq test-data/testout.join.fastq test-data/testout.un1.fastq test-data/testout.un2.fastq tool_dependencies.xml
diffstat 7 files changed, 207 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq-join.xml	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,65 @@
+<tool id="fastq_join" name="fastq-join" version="0.1">
+    <description> - Joins two paired-end reads on the overlapping ends</description>
+    <requirements>
+        <requirement type="package" version="1.1.2-469">ea-utils</requirement>
+    </requirements>
+    <command>
+        fastq-join 
+        -v '$splitChar'
+        -p $pctMaxDiff
+        -m $minOverlap
+        #if $stitchLengthReport:
+        -r $outputStitchLengthReport
+        #end if
+        $read1
+        $read2
+        -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined 
+    </command>
+    <inputs>
+        <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
+        <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
+        <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
+        <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
+        <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
+        <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
+    </inputs>
+
+    <outputs>
+        <data format="input" format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
+        <data format="input" format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
+        <data format="input" format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
+        <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
+            <filter>stitchLengthReport</filter>
+        </data>
+    </outputs>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
+    </stdio>
+
+    <tests>
+        <test>
+            <param name="read1" value="test_read1.fastq" />
+            <param name="read2" value="test_read3.fastq" />
+            <output name="outputJoined" file="testout.join.fastq" />
+            <output name="outputUnmatched1" file="testout.un1.fastq" />
+            <output name="outputUnmatched2" file="testout.un2.fastq" />
+        </test>
+    </tests>
+
+    <help>
+Overview
+--------
+fastq-join joins two paired-end reads on the overlapping ends.
+
+Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads.
+
+Maximum difference is the maximum allowed percentage of bases that differ in the matching region.
+
+Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined.
+
+Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
+
+This tool uses sqr(distance)/len for anchored alignment quality algorithm. It's a good measure of anchored alignment quality, akin to squared-deviation for means.  This tool uses the fastq-join program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/FastqJoin for details.
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_read1.fastq	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,40 @@
+@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+?+:BDDDAD8BDD?@4+<?EECD?BBFIDFD<E:*?DI@?DDEDDCEECEIECDCCAD>5;6?;;@A;AABA>A@>AAAD;A>A>5=5>>>BBAA######
+@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 1:N:0:
+GTGATAGAGATACTGAGCACAGAGCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@?BDFFFFHBHHHJJJGFEHHEIHEGHJJJJDI@DHIIHGGGGGEHIHGIIIIJJJGIB?AACBEDDFCDCCCCCEDC>@CD>CC@BA>CDEECD=BDDB>
+@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIII?EEEDFFFFEEEEEDECDDDEDDDDCCBACDEDECC@BB9<A
+@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACGTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+B?@DFFFFHHHHHGIIJIIJJJJJJIJJJJJIIHIJJIJJIIGGJJGHGHIGGIIJHIGAEEEDFFEEEEFEEDDDDDCC>CCCCCACDDEEDCA9>BBDC
+@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@<EFHA?DDFFDHHHHCHIIIIGGGH-;@5=CHHEADDEBEECCCCDCA@CCCB@CC@BC(;';BBBC
+@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGCATATACCGCCAAT
++
+B=BDFFFFHGHHHJJIIJHIJIIJJJJJJJJIJIJJJIIJJHIIIJJJJIIIIJJIGJJ??CBBFFFFEDEEEEECDDCDDDCDCC@BDCDDEEC><>BD?
+@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C
+@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@=@DFDFFHAHDHGFEE@FFHGGEDEGHGIJ@GFGHAGFIIGBDGHIIJIGJJJJJIIIACEBDEFDFDEEEEDEDDCCDCD;CDCB@CF@DD@C?B<@DC
+@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@:?DDDDDF<FHHIIEEGBHGGDGGIIIGHIIIGGGHGEHFIHGIIIII<HHHIEGGIIHE=?BDECD@CDDCCCCCAAC@ACACCBCCDCDDDC######
+@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@@@DFFFFHFHHGIJIJJJJJIJJJJIIIJJIIJJIJIEHIHIEHHIGJEHIIJIJDCGCE?BFFFDFEDDEEECACCCDDD@C>ABCCDCFFCA:9BBBC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_read3.fastq	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,40 @@
+@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+BB8=4ADDHHHHACG<FHIGGIIIIICAEEC;CDF0@DEG3?BBACCGGICFD@@;@7;AED<<=CC@>(;(;@C@C:<:>>@>>;B>B(44?>C@B9<<8
+@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+@?=DDDFFDFHHHIGGHHIGGFEGIJJFAFEGGGH@AFFHGIIIGEFHBF>@FCGAE@DD=D'9@DCC@;C@C@CDDCD>CCD@>>:@@C@CDDACA<28?
+@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+CCCFFFFFHHHHHJIIJJJJJJIJJJJIJJJJJJJIJJJJJJJJJJJJJJIHIJJIJEEHHF>BBDEFEDDDDDDDCDDDDCDDDEEEEDDDDDDDBDBDD
+@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+B@@DDFFFGHHHDIFHIJIIIJJJJIJJJJJIJJIIJIJIGIIJGIJJJJDFGGGII:DHFF<BDECDEDD@CCCDDCDDDCEDDDDC@C@CCDCD?@8<<
+@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+@;?DFDFFFDHHDIGACFHGGGGJJEH3@GDGCGHIEIIG?FDHCEGHEI9@C@C@@@9@=<',5;5;;;AC>3>C>CCCC(5(;>CDECCAC>@AB08AB
+@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATGCTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+C@@FFFFFHHHHHJJJJJIJIJJJJIIJJIJIIFIGIJGHIDGIIIGIJJIHGHIIJGIIHF<<@DDDDEEDDCCCDDDCCCDDDEDDEDDCCDDCBB?AB
+@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0:
+TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC
++
+#####################################################################################################
+@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+@@@DDFFFHHHHFEEGIEHIJJGGFGIGIHCHJJJJJJIJIJGIGGIJIJGCDGEGG>EGHF=ABC@BDDCDDA@CCCCDCDE@CCD>CC@CDDDDBD?<<
+@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGATAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+CC@FFFFFGFHDDHH>@FHHCHIIGIIEGGHIJIIBEEHIGGGGJIJJJJGBFGIGGCAHEA,9?B>B@@C>@@ACACCCC@C@@CDCDC@>CCCDD@(8?
+@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 3:N:0:
+TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA
++
+CCCFFFFFHHHGHJJJJJIJJJJJIJJJHIJJIJJIIGIIIJEIIJIIJIG@FHIJJJIJHF<A?CBCC>CCDCCDDDDDDCDCCDDEACA@CDDDDDABB
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout.join.fastq	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,36 @@
+@JLK5VL1:222:D1888ACXX:1:1101:1656:2143
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+?+:BDDDAD8BDD?@4+<?EECD?BBFIDFD<E:*?DI@?DDEDDCEECEIECDCCADB@C>?;;@B>BABA@A@>AACDCA>A>5>@CC>BBDEA;7@;@@DFCIGGCCABB?3GED@0FDC;CEEACIIIIIGGIHF<GCAHHHHDDA4=8BB
+@JLK5VL1:222:D1888ACXX:1:1101:1613:2167
+GTGATAGAGATACTGAGCACAGAGCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@?BDFFFFHBHHHJJJGFEHHEIHEGHJJJJDI@DHIIHGGGGGEHIHGIIIIJJJGIBCADDCEDDFCDCCDCCEDCDDCDCCC@BCCDDEEDDDDDEBGCF@>FBHFEGIIIGHFFA@HGGGEFAFJJIGEFGGIHHGGIHHHFDFFDDD=?@
+@JLK5VL1:222:D1888ACXX:1:1101:1927:2121
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIIIDEEEDFFFFEEEEEDEDDDDEDDDDDDEFEDEDEFHHEEJIJJIHIJJJJJJJJJJJJJJIJJJJJJJIJJJJIJJJJJJIIJHHHHHFFFFFCCC
+@JLK5VL1:222:D1888ACXX:1:1101:2000:2166
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACGTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+B?@DFFFFHHHHHGIIJIIJJJJJJIJJJJJIIHIJJIJJIIGGJJGHGHIGGIIJHIGDEEEDFFEEEEFEEDDDDDDDCCCCDDEDDEEEDFFHDBIIGGGFDJJJJIGJIIGIJIJIIJJIJJJJJIJJJJIIIJIHFIDHHHGFFFDD@@B
+@JLK5VL1:222:D1888ACXX:1:1101:1763:2172
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@<EFHA?DDFFDHHHHCHIIIIGGGHA@@CACHHECDDEBEECCCCDCA@CCCB@CC@BC<=@;BBBC@C@9IEHGECHDF?GIIEIHGCGDG@3HEJJGGGGHFCAGIDHHDFFFDFD?;@
+@JLK5VL1:222:D1888ACXX:1:1101:1832:2198
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGCATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+B=BDFFFFHGHHHJJIIJHIJIIJJJJJJJJIJIJJJIIJJHIIIJJJJIIIIJJIGJJCDDCCFFFFEEEEEEECDDDDDDDDEEDDDDDDEFHIIGJIIHGHIJJIGIIIGDIHGJIGIFIIJIJJIIJJJJIJIJJJJJHHHHHFFFFF@@C
+@JLK5VL1:222:D1888ACXX:1:1101:2236:2214
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@=@DFDFFHAHDHGFEE@FFHGGEDEGHGIJ@GFGHAGFIIGBDGHIIJIGJJJJJIIIDDEDDEFDFDEEEEDEDDCCDCDDDDDDBCFBDDFHGE>GGEGDCGJIJIGGIGJIJIJJJJJJHCHIGIGFGGJJIHEIGEEFHHHHFFFDD@@@
+@JLK5VL1:222:D1888ACXX:1:1101:2090:2240
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTATCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@:?DDDDDF<FHHIIEEGBHGGDGGIIIGHIIIGGGHGEHFIHGIIIII<HHHIEGGIIHECCBDEDDDCDDCCCCCCACAACACCBCCDCDDDEHACGGIGFBGJJJJIJGGGGIHEEBIIJIHGGEIIGIIHCHHF@>HHDDHFGFFFFF@CC
+@JLK5VL1:222:D1888ACXX:1:1101:2952:2161
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA
++
+@@@DFFFFHFHHGIJIJJJJJIJJJJIIIJJIIJJIJIEHIHIEHHIGJEHIIJIJDDGDEDCFFFDFEDDEEEDDDDDDDDDCCACCCDCFFFHJIJJJIHF@GIJIIJIIEJIIIGIIJJIJJIHJJJIJJJJJIJJJJJHGHHHFFFFFCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout.un1.fastq	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,4 @@
+@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0:
+GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT
++
+@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout.un2.fastq	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,4 @@
+@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0:
+TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC
++
+#####################################################################################################
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 20 18:59:38 2012 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ea-utils" version="1.1.2-469">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://ea-utils.googlecode.com/files/ea-utils.1.1.2-469.tar.gz</action>
+                <!-- sam-stats and varcall require an extra Bamtools library and we don't need them, so skip -->
+                <action type="shell_command">sed -i.bak 's/sam-stats varcall$//' Makefile</action>
+                <action type="shell_command">PREFIX=$INSTALL_DIR make install</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>