| Previous changeset 0:0ad51e73587e (2016-12-02) Next changeset 2:57a00c4e43ec (2017-03-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 772d7fb670aaa4ad131909bf2aef5d7dd016e621 |
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modified:
nugen_nudup.xml |
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added:
test-data/nudup_umis.fastq.gz |
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| diff -r 0ad51e73587e -r 24693e595caf nugen_nudup.xml --- a/nugen_nudup.xml Fri Dec 02 18:03:47 2016 -0500 +++ b/nugen_nudup.xml Sat Feb 25 01:38:55 2017 -0500 |
| [ |
| @@ -1,19 +1,31 @@ -<tool id="nugen_nudup" name="NuDUP" version="2.2_post2016104"> - <description>mark/remove PCR duplicates based on molecular tags</description> +<tool id="nugen_nudup" name="NuDUP" version="2.3.1" profile="17.01"> + <description> + mark/remove PCR duplicates based on molecular tags + </description> <requirements> - <requirement type="package" version="2.2_post2016104">nudup</requirement> + <requirement type="package" version="2.3.1">nudup</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <version_command>nudup.py --version</version_command> <command><![CDATA[ - ln -f -s '$input' 'input.bam' && - ln -f -s '$input.metadata.bam_index' 'input.bai' && - nudup.py $paired_end - -f '$umi_fastq' + ln -f -s '$input' 'input.bam' && + ln -f -s '$input.metadata.bam_index' 'input.bai' && + mkdir 'tmp' && + #if $umi_fastq.is_of_type('fastq.gz','fastqsanger.gz'): + #set umi_file = 'umi.fastq.gz' + #else: + #set umi_file = 'umi.fastq' + #end if + ln -f -s '$umi_fastq' '$umi_file' && + nudup.py + -T \$PWD'/tmp' + $paired_end + -f '$umi_file' --start $start --length $length + $rmdup_only 'input.bam' ]]> </command> @@ -21,8 +33,9 @@ <param type="data" name="input" label="Input SAM/BAM file" format="sam,bam" help="Input SAM/BAM containing only unique alignments" /> - <param type="data" name="umi_fastq" label="Fastq file containing - molecular tag sequence" format="fastq,fastqsanger" help="FASTQ + <param type="data" name="umi_fastq" + label="Fastq file containing molecular tag sequence" + format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ file containing the molecular tag sequence for each read name in the corresponding SAM/BAM file" /> <param type="boolean" argument="--paired-end" @@ -38,16 +51,40 @@ counts in from the 3' END of the read." /> <param type="integer" argument="--length" label="Tag sequence length" value="6" help="length of molecular tag sequence" /> + <param type="boolean" argument="--rmdup-only" name="rmdup_only" + label="Only output BAM with duplicates removed" + truevalue="--rmdup-only" falsevalue="" checked="false" + help="Do not ouput BAM with duplicates marked. Default is to ouput + both marked duplicates and removed duplicates BAM files." /> </inputs> <outputs> - <data format="bam" name="markdup" from_work_dir="prefix.sorted.markdup.bam" /> - <data format="bam" name="dedup" from_work_dir="prefix.sorted.dedup.bam" /> - <data format="txt" name="log" from_work_dir="prefix_dup_log.txt" /> + <data format="bam" name="markdup" metadata_source="input" + label="${tool.name} on ${on_string}: MarkDup" + from_work_dir="prefix.sorted.markdup.bam"> + <filter>not rmdup_only</filter> + </data> + <data format="bam" name="dedup" metadata_source="input" + label="${tool.name} on ${on_string}: DeDup" + from_work_dir="prefix.sorted.dedup.bam" /> + <data format="txt" name="log" + label="${tool.name} on ${on_string}: Log" + from_work_dir="prefix_dup_log.txt" /> </outputs> <tests> <test> <param name="input" value="nudup_test_1.bam" ftype="bam" /> - <param name="umi_fastq" value="nudup_umis.fastq" ftype="fastqsanger" /> + <param name="umi_fastq" value="nudup_umis.fastq" + ftype="fastqsanger" /> + <param name="start" value="8" /> + <param name="length" value="8" /> + <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" /> + <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" /> + <output name="log" file="nudup_log_1.txt" ftype="txt" /> + </test> + <test> + <param name="input" value="nudup_test_1.bam" ftype="bam" /> + <param name="umi_fastq" value="nudup_umis.fastq.gz" + ftype="fastqsanger.gz" /> <param name="start" value="8" /> <param name="length" value="8" /> <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" /> @@ -97,18 +134,23 @@ from the 3' END of the read. (default = 6) -l LENGTH, --length LENGTH length of molecular tag sequence (default = 6) + -T TEMP_DIR directory for reading and writing to temporary files + and named pipes (default: /tmp) + --old-samtools required for compatibility with samtools sort style in + samtools versions <=0.1.19 + --rmdup-only required for only outputting duplicates removed file -v, --version show program's version number and exit -h, --help show this help message and exit ]]></help> <citations> - <citation type="bibtex">@misc{Patel2016, + <citation type="bibtex">@misc{Patel2017, author = {Patel, Anand}, title = {NuDUP}, - year = {2016}, + year = {2017}, publisher = {GitHub}, journal = {GitHub repository}, howpublished = {\url{https://github.com/nugentechnologies/nudup}}, - commit = {740d9fe439dd8917605a56483a8796b377eb24c6} + commit = {7451de86680d24f19638ed6ac88f6504f0817753} } </citation> </citations> |
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| diff -r 0ad51e73587e -r 24693e595caf test-data/nudup_umis.fastq.gz |
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| Binary file test-data/nudup_umis.fastq.gz has changed |