changeset 10:5d969cb56112

Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
author lparsons
date Fri, 07 Dec 2012 14:35:44 -0500
parents 971e20519fb8
children f320093f1e8e
files htseq-count.xml test-data/htseq-test-paired.bam test-data/htseq-test-paired_counts.tsv test-data/htseq-test-paired_othercounts.tsv test-data/htseq-test_counts.tsv test-data/htseq-test_othercounts.tsv tool_dependencies.xml
diffstat 7 files changed, 188 insertions(+), 7013 deletions(-) [+]
line wrap: on
line diff
--- a/htseq-count.xml	Fri Oct 26 15:57:08 2012 -0400
+++ b/htseq-count.xml	Fri Dec 07 14:35:44 2012 -0500
@@ -1,10 +1,11 @@
-<tool id="htseq_count" name="htseq-count" version="0.2.1">
+<tool id="htseq_count" name="htseq-count" version="0.3">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
         <requirement type="package" version="1.6.2">numpy</requirement>
         <requirement type="package" version="0.5.3p9">htseq</requirement>
         <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.56.0">picard</requirement> 
     </requirements>
     <command>
     ##set up input files
@@ -17,9 +18,16 @@
             #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
         #end if
     #end if
-
-    #if $samfile.extension == "bam":
-        samtools view $samfile | 
+    #if str($singlepaired) == "paired":
+        ln -s $samfile local_input.sam &amp;&amp;
+        java -Xmx2G -jar "\$JAVA_JAR_PATH/SortSam.jar" VALIDATION_STRINGENCY=LENIENT SORT_ORDER=queryname O=prepared_input.sam I=local_input.sam TMP_DIR="${__new_file_path__}" 
+        || echo "Error running Picard MergeSamFiles" &gt;&amp;2 &amp;&amp;
+    #else:
+        #if $samfile.extension == "bam":
+            samtools view $samfile | 
+        #else
+            ln -s $samfile prepared_input.sam &amp;&amp;
+        #end if
     #end if
     htseq-count 
     --mode=$mode 
@@ -30,19 +38,26 @@
     #if $samout_conditional.samout:
         --samout=$__new_file_path__/${samoutfile.id}_tmp
     #end if
-    #if $samfile.extension == "bam":
-        - 
-    #else
-        $samfile 
-    #end if
+    #if str($singlepaired) == "paired":
+        prepared_input.sam
+    #else:
+        #if $samfile.extension == "bam":
+            - 
+        #else:
+            prepared_input.sam
+        #end if
+    #end if    
     $gfffile 
     | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&amp;2"; else print $0}' &gt; $counts 2&gt;$othercounts
     #if $samout_conditional.samout:
         &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
     #end if</command>
     <inputs>
-        <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File">
-            <help>Paired-End data MUST be sorted by QUERY NAME, use "NGS: Picard - Paired Read Mate Fixer" to sort by QUERY NAME and output to SAM (not BAM) before using this tool on paired data.</help>
+        <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
+        <param name="singlepaired" type="select" label="Is this library mate-paired?">
+            <help>Paired libraries will be sorted by read name prior to counting.</help>
+            <option value="single" selected="true">single-end</option>
+            <option value="paired">paired-end</option>
         </param>
         <param format="gff" name="gfffile" type="data" label="GFF File"/>
         <param name="mode" type="select" label="Mode">
@@ -93,9 +108,9 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/>
-        <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/>
-        <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)">
+        <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
+        <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
+        <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
             <filter>samout_conditional['samout']</filter>
         </data>
     </outputs>
@@ -107,6 +122,7 @@
         <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
         <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
         <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
+        <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. \(Is the SAM file properly sorted\?\)" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the paired-end option. See stderr output of this dataset for more information." />
     </stdio>
 
     <tests>
@@ -124,6 +140,14 @@
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
+        <test>
+            <param name="samfile" value="htseq-test-paired.bam" />
+            <param name="singlepaired" value="paired" />
+            <param name="gfffile" value="htseq-test.gff" />
+            <param name="samout" value="False" />
+            <output name="counts" file="htseq-test-paired_counts.tsv" />
+            <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
+        </test>
         <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
         <test>
             <param name="samfile" value="htseq-test.sam" />
Binary file test-data/htseq-test-paired.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq-test-paired_counts.tsv	Fri Dec 07 14:35:44 2012 -0500
@@ -0,0 +1,127 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq-test-paired_othercounts.tsv	Fri Dec 07 14:35:44 2012 -0500
@@ -0,0 +1,5 @@
+no_feature	533
+ambiguous	1
+too_low_aQual	0
+not_aligned	0
+alignment_not_unique	0
--- a/test-data/htseq-test_counts.tsv	Fri Oct 26 15:57:08 2012 -0400
+++ b/test-data/htseq-test_counts.tsv	Fri Dec 07 14:35:44 2012 -0500
@@ -1,60 +1,4 @@
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@@ -176,6949 +120,8 @@
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-snR85	0
-snR86	1
-snR87	0
-snR9	1
-tA(AGC)D	0
-tA(AGC)F	0
-tA(AGC)G	0
-tA(AGC)H	0
-tA(AGC)J	0
-tA(AGC)K1	0
-tA(AGC)K2	0
-tA(AGC)L	0
-tA(AGC)M1	0
-tA(AGC)M2	0
-tA(AGC)P	0
 tA(UGC)A	0
-tA(UGC)E	0
-tA(UGC)G	0
-tA(UGC)L	0
-tA(UGC)O	0
-tA(UGC)Q	0
-tC(GCA)B	0
-tC(GCA)G	0
-tC(GCA)P1	0
-tC(GCA)P2	0
-tC(GCA)Q	0
-tD(GUC)B	0
-tD(GUC)D	0
-tD(GUC)G1	0
-tD(GUC)G2	0
-tD(GUC)I1	0
-tD(GUC)I2	0
-tD(GUC)J1	0
-tD(GUC)J2	0
-tD(GUC)J3	0
-tD(GUC)J4	0
-tD(GUC)K	0
-tD(GUC)L1	0
-tD(GUC)L2	0
-tD(GUC)M	0
-tD(GUC)N	0
-tD(GUC)O	0
-tD(GUC)Q	0
-tE(CUC)D	0
-tE(CUC)I	0
-tE(UUC)B	0
-tE(UUC)C	0
-tE(UUC)E1	0
-tE(UUC)E2	0
-tE(UUC)E3	0
-tE(UUC)G1	0
-tE(UUC)G2	0
-tE(UUC)G3	0
-tE(UUC)I	0
-tE(UUC)J	0
-tE(UUC)K	0
-tE(UUC)L	0
-tE(UUC)M	0
-tE(UUC)P	0
-tE(UUC)Q	0
-tF(GAA)B	0
-tF(GAA)D	0
-tF(GAA)F	0
-tF(GAA)G	0
-tF(GAA)H1	0
-tF(GAA)H2	0
-tF(GAA)M	0
-tF(GAA)N	0
-tF(GAA)P1	0
-tF(GAA)P2	0
-tF(GAA)Q	0
-tG(CCC)D	0
-tG(CCC)O	0
-tG(GCC)B	0
-tG(GCC)C	0
-tG(GCC)D1	0
-tG(GCC)D2	0
-tG(GCC)E	0
-tG(GCC)F1	0
-tG(GCC)F2	0
-tG(GCC)G1	0
-tG(GCC)G2	0
-tG(GCC)J1	0
-tG(GCC)J2	0
-tG(GCC)M	0
-tG(GCC)O1	0
-tG(GCC)O2	0
-tG(GCC)P1	0
-tG(GCC)P2	0
-tG(UCC)G	0
-tG(UCC)N	0
-tG(UCC)O	0
-tG(UCC)Q	0
-tH(GUG)E1	0
-tH(GUG)E2	0
-tH(GUG)G1	0
-tH(GUG)G2	0
-tH(GUG)H	0
-tH(GUG)K	0
-tH(GUG)M	0
-tH(GUG)Q	0
-tI(AAU)B	0
-tI(AAU)D	0
-tI(AAU)E1	0
-tI(AAU)E2	0
-tI(AAU)G	0
-tI(AAU)I1	0
-tI(AAU)I2	0
-tI(AAU)L1	0
-tI(AAU)L2	0
-tI(AAU)N1	0
-tI(AAU)N2	0
-tI(AAU)P1	0
-tI(AAU)P2	0
-tI(GAU)Q	0
-tI(UAU)D	0
-tI(UAU)L	0
-tK(CUU)C	0
-tK(CUU)D1	0
-tK(CUU)D2	0
-tK(CUU)E1	0
-tK(CUU)E2	0
-tK(CUU)F	0
-tK(CUU)G1	0
-tK(CUU)G2	0
-tK(CUU)G3	0
-tK(CUU)I	0
-tK(CUU)J	0
-tK(CUU)K	0
-tK(CUU)M	0
-tK(CUU)P	0
-tK(UUU)D	0
-tK(UUU)G1	0
-tK(UUU)G2	0
-tK(UUU)K	0
-tK(UUU)L	0
-tK(UUU)O	0
-tK(UUU)P	0
-tK(UUU)Q	0
 tL(CAA)A	0
-tL(CAA)C	0
-tL(CAA)D	0
-tL(CAA)G1	0
-tL(CAA)G2	0
-tL(CAA)G3	0
-tL(CAA)K	0
-tL(CAA)L	0
-tL(CAA)M	0
-tL(CAA)N	0
-tL(GAG)G	0
-tL(UAA)B1	0
-tL(UAA)B2	0
-tL(UAA)D	0
-tL(UAA)J	0
-tL(UAA)K	0
-tL(UAA)L	0
-tL(UAA)N	0
-tL(UAA)Q	0
-tL(UAG)J	0
-tL(UAG)L1	0
-tL(UAG)L2	0
-tM(CAU)C	0
-tM(CAU)D	0
-tM(CAU)E	0
-tM(CAU)J1	0
-tM(CAU)J2	0
-tM(CAU)J3	0
-tM(CAU)M	0
-tM(CAU)O1	0
-tM(CAU)O2	0
-tM(CAU)P	0
-tM(CAU)Q1	0
-tM(CAU)Q2	0
-tN(GUU)C	0
-tN(GUU)F	0
-tN(GUU)G	0
-tN(GUU)K	0
-tN(GUU)L	0
-tN(GUU)N1	0
-tN(GUU)N2	0
-tN(GUU)O1	0
-tN(GUU)O2	0
-tN(GUU)P	0
-tN(GUU)Q	0
-tP(AGG)C	0
-tP(AGG)N	0
 tP(UGG)A	0
-tP(UGG)F	0
-tP(UGG)H	0
-tP(UGG)L	0
-tP(UGG)M	0
-tP(UGG)N1	0
-tP(UGG)N2	0
-tP(UGG)O1	0
-tP(UGG)O2	0
-tP(UGG)O3	0
-tP(UGG)Q	0
-tQ(CUG)M	0
-tQ(UUG)B	0
-tQ(UUG)C	0
-tQ(UUG)D1	0
-tQ(UUG)D2	0
-tQ(UUG)D3	0
-tQ(UUG)E1	0
-tQ(UUG)E2	0
-tQ(UUG)H	0
-tQ(UUG)L	0
-tQ(UUG)Q	0
-tR(ACG)D	0
-tR(ACG)E	0
-tR(ACG)J	0
-tR(ACG)K	0
-tR(ACG)L	0
-tR(ACG)O	0
-tR(ACG)Q2	0
-tR(CCG)L	0
-tR(CCU)J	0
-tR(UCU)B	0
-tR(UCU)D	0
-tR(UCU)E	0
-tR(UCU)G1	0
-tR(UCU)G2	0
-tR(UCU)G3	0
-tR(UCU)J1	0
-tR(UCU)J2	0
-tR(UCU)K	0
-tR(UCU)M1	0
-tR(UCU)M2	0
-tR(UCU)Q1	0
 tS(AGA)A	0
-tS(AGA)B	0
-tS(AGA)D1	0
-tS(AGA)D2	0
-tS(AGA)D3	0
-tS(AGA)E	0
-tS(AGA)G	0
-tS(AGA)H	0
-tS(AGA)J	0
-tS(AGA)L	0
-tS(AGA)M	0
-tS(CGA)C	0
-tS(GCU)F	0
-tS(GCU)L	0
-tS(GCU)O	0
-tS(GCU)Q1	0
-tS(UGA)E	0
-tS(UGA)I	0
-tS(UGA)P	0
-tS(UGA)Q2	0
-tT(AGU)B	0
-tT(AGU)C	0
-tT(AGU)D	0
-tT(AGU)H	0
-tT(AGU)I1	0
-tT(AGU)I2	0
-tT(AGU)J	0
-tT(AGU)N1	0
-tT(AGU)N2	0
-tT(AGU)O1	0
-tT(AGU)O2	0
-tT(CGU)K	0
-tT(UGU)G1	0
-tT(UGU)G2	0
-tT(UGU)H	0
-tT(UGU)P	0
-tT(UGU)Q1	0
-tT(XXX)Q2	0
-tV(AAC)E1	0
-tV(AAC)E2	0
-tV(AAC)G1	0
-tV(AAC)G2	0
-tV(AAC)G3	0
-tV(AAC)H	0
-tV(AAC)J	0
-tV(AAC)K1	0
-tV(AAC)K2	0
-tV(AAC)L	0
-tV(AAC)M1	0
-tV(AAC)M2	0
-tV(AAC)M3	0
-tV(AAC)O	0
-tV(CAC)D	0
-tV(CAC)H	0
-tV(UAC)B	0
-tV(UAC)D	0
-tV(UAC)Q	0
-tW(CCA)G1	0
-tW(CCA)G2	0
-tW(CCA)J	0
-tW(CCA)K	0
-tW(CCA)M	0
-tW(CCA)P	0
-tW(UCA)Q	0
-tX(XXX)D	0
-tY(GUA)D	0
-tY(GUA)F1	0
-tY(GUA)F2	0
-tY(GUA)J1	0
-tY(GUA)J2	0
-tY(GUA)M1	0
-tY(GUA)M2	0
-tY(GUA)O	0
-tY(GUA)Q	0
--- a/test-data/htseq-test_othercounts.tsv	Fri Oct 26 15:57:08 2012 -0400
+++ b/test-data/htseq-test_othercounts.tsv	Fri Dec 07 14:35:44 2012 -0500
@@ -1,5 +1,5 @@
-no_feature	1437
-ambiguous	67
+no_feature	19
+ambiguous	0
 too_low_aQual	0
 not_aligned	1336
 alignment_not_unique	0
--- a/tool_dependencies.xml	Fri Oct 26 15:57:08 2012 -0400
+++ b/tool_dependencies.xml	Fri Dec 07 14:35:44 2012 -0500
@@ -55,4 +55,20 @@
             Compiling SAMtools requires the ncurses and zlib development libraries.
         </readme>
     </package>
+    <package name="picard" version="1.56.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>picard-tools-1.56</source_directory>
+                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
 </tool_dependency>