Mercurial > repos > lparsons > htseq_count
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(-) [+] |
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--- 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 $samfile local_input.sam && + java -Xmx2G -jar "\$JAVA_JAR_PATH/SortSam.jar" VALIDATION_STRINGENCY=LENIENT SORT_ORDER=queryname O=prepared_input.sam I=local_input.sam TMP_DIR="${__new_file_path__}" + || echo "Error running Picard MergeSamFiles" >&2 && + #else: + #if $samfile.extension == "bam": + samtools view $samfile | + #else + ln -s $samfile prepared_input.sam && + #end if #end if htseq-count --mode=$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>&2"; else print $0}' > $counts 2>$othercounts #if $samout_conditional.samout: && 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" />
--- /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 @@ +HRA1 2 +YAL001C 12 +YAL002W 6 +YAL003W 5 +YAL004W 3 +YAL005C 5 +YAL007C 1 +YAL008W 0 +YAL009W 2 +YAL010C 3 +YAL011W 2 +YAL012W 3 +YAL013W 3 +YAL014C 5 +YAL015C 5 +YAL016C-A 0 +YAL016C-B 1 +YAL016W 2 +YAL017W 8 +YAL018C 5 +YAL019W 1 +YAL019W-A 0 +YAL020C 0 +YAL021C 10 +YAL022C 4 +YAL023C 5 +YAL024C 13 +YAL025C 1 +YAL026C 6 +YAL026C-A 0 +YAL027W 3 +YAL028W 3 +YAL029C 10 +YAL030W 1 +YAL031C 4 +YAL031W-A 2 +YAL032C 3 +YAL033W 2 +YAL034C 0 +YAL034C-B 2 +YAL034W-A 2 +YAL035W 7 +YAL036C 4 +YAL037C-A 0 +YAL037C-B 3 +YAL037W 1 +YAL038W 4 +YAL039C 1 +YAL040C 3 +YAL041W 8 +YAL042C-A 1 +YAL042W 5 +YAL043C 9 +YAL044C 0 +YAL044W-A 0 +YAL045C 0 +YAL046C 2 +YAL047C 2 +YAL047W-A 0 +YAL048C 7 +YAL049C 1 +YAL051W 3 +YAL053W 5 +YAL054C 2 +YAL055W 3 +YAL056C-A 0 +YAL056W 7 +YAL058W 4 +YAL059C-A 6 +YAL059W 4 +YAL060W 1 +YAL061W 4 +YAL062W 4 +YAL063C 0 +YAL063C-A 0 +YAL064C-A 0 +YAL064W 0 +YAL064W-B 0 +YAL065C 2 +YAL066W 0 +YAL067C 8 +YAL067W-A 1 +YAL068C 1 +YAL068W-A 0 +YAL069W 0 +YAR002C-A 0 +YAR002W 1 +YAR003W 4 +YAR007C 7 +YAR008W 0 +YAR009C 1 +YAR010C 0 +YAR014C 4 +YAR015W 4 +YAR018C 4 +YAR019C 4 +YAR019W-A 3 +YAR020C 0 +YAR023C 1 +YAR027W 0 +YAR028W 3 +YAR029W 0 +YAR030C 2 +YAR031W 4 +YAR033W 0 +YAR035C-A 0 +YAR035W 3 +YAR042W 4 +YAR047C 0 +YAR050W 4 +YAR053W 0 +YAR060C 2 +YAR061W 0 +YAR062W 2 +YAR064W 1 +YAR066W 2 +YAR068W 2 +YAR069C 1 +YAR070C 0 +YAR071W 4 +YAR073W 1 +YAR075W 0 +snR18 0 +tA(UGC)A 0 +tL(CAA)A 1 +tP(UGG)A 2 +tS(AGA)A 3
--- /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 @@ -15S_rRNA 0 -21S_rRNA 0 HRA1 0 -LSR1 0 -NME1 0 -Q0010 0 -Q0017 0 -Q0032 0 -Q0045 0 -Q0050 0 -Q0055 0 -Q0060 0 -Q0065 0 -Q0070 0 -Q0075 0 -Q0080 0 -Q0085 0 -Q0092 0 -Q0105 0 -Q0110 0 -Q0115 0 -Q0120 0 -Q0130 0 -Q0140 0 -Q0142 0 -Q0143 0 -Q0144 0 -Q0160 0 -Q0182 0 -Q0250 0 -Q0255 0 -Q0275 0 -Q0297 0 -R0010W 3 -R0020C 14 -R0030W 1 -R0040C 20 -RDN18-1 205 -RDN18-2 2 -RDN25-1 1408 -RDN25-2 59 -RDN5-1 0 -RDN5-2 1 -RDN5-3 0 -RDN5-4 0 -RDN5-5 3 -RDN5-6 0 -RDN58-1 85 -RDN58-2 1 -RNA170 0 -RPM1 0 -RPR1 0 -RUF5-1 0 -RUF5-2 0 -SCR1 0 -SRG1 1 -TLC1 0 YAL001C 3 YAL002W 2 YAL003W 31 @@ -176,6949 +120,8 @@ YAR071W 1 YAR073W 0 YAR075W 0 -YBL001C 2 -YBL002W 6 -YBL003C 20 -YBL004W 8 -YBL005W 2 -YBL005W-A 0 -YBL005W-B 3 -YBL006C 1 -YBL006W-A 0 -YBL007C 4 -YBL008W 2 -YBL008W-A 0 -YBL009W 3 -YBL010C 1 -YBL011W 4 -YBL012C 0 -YBL013W 0 -YBL014C 0 -YBL015W 0 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--- 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>