Mercurial > repos > thanhlv > qc3c
changeset 0:64d1f6186527 draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/qc3c commit bd5512047445d9a39a198b7cffeba78fe7b9d140-dirty
| author | thanhlv |
|---|---|
| date | Mon, 07 Oct 2019 04:37:02 -0400 |
| parents | |
| children | |
| files | macros.xml qc3c_bam.xml qc3c_kmer.xml |
| diffstat | 3 files changed, 129 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 07 04:37:02 2019 -0400 @@ -0,0 +1,17 @@ +<macros> + <token name="@VERSION@">0.2.6.3</token> + <xml name="requirements"> + <requirements> + <container type="singularity">path/to/qc3c.sif</container> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>bin3C -V | grep -E -o "([0-9]\.[0-9]\.[0-9]\.[0-9])"</version_command> + </xml> + <!-- <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13059-019-1643-1</citation> + </citations> + </xml> --> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qc3c_bam.xml Mon Oct 07 04:37:02 2019 -0400 @@ -0,0 +1,52 @@ +<tool id="qc3c_bam" name="qc3c_bam" version="@VERSION@"> + <description>qc3C Alignment-based analysis</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + qc3C bam + -p $sample_rate + -s $seed + --write_report + $verbose + -t \${GALAXY_SLOTS:-1} + --output-path './out' + -m $mean_insert + -q $min_mapq + #if str($neb_name) != "": + #for $enzyme in str($neb_name).split(',') + -e $enzyme + #end for + #end if + -b $bam + ]]></command> + + <inputs> + <param name="bam" type="data" format="bam" label="Input name-sorted bam file of Hi-C reads mapped to references" /> + <param name="sample_rate" type="float" min="0" value="0" label="Sample only a proportion of all read-pairs"/> + <param name="seed" type="integer" min="1" value="20191902" label="Minimum cluster extent used in output"/> + <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" /> + <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" /> + <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for + multiple enzymes" /> + <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Create a result report in JSONLines format" /> + </inputs> + + <outputs> + <data name="report" format="json" label="{tool.name} on ${on_string} Report" from_work_dir="out/report.jsonl"/> + <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/qc3C.log"/> + </outputs> + + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + + Documentation can be found at `<https://github.com/cerebis/bin3C>`_. + + ]]></help> +<expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qc3c_kmer.xml Mon Oct 07 04:37:02 2019 -0400 @@ -0,0 +1,60 @@ +<tool id="qc3c_kmer" name="qc3c_kmer" version="@VERSION@"> + <description>qc3C Kmer-based analysis</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + jellyfish count -m $kmer_size -s 2G -C -o kmers.jf $fastq && + + qc3C kmer + #if str($sample_rate) != "0": + -p $sample_rate + #end if + -s $seed + --write_report + $verbose + -t \${GALAXY_SLOTS:-1} + --output-path './out' + -m $mean_insert + --output-table table.tsv + -x $max_coverage + -l kmers.jf + #if str($neb_name) != "": + #for $enzyme in str($neb_name).split(',') + -e $enzyme + #end for + #end if + -r $fastq + ]]></command> + + <inputs> + <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FastQ format reads" /> + <param name="sample_rate" type="float" min="0" value="0" label="Sample only a proportion of all read-pairs"/> + <param name="seed" type="integer" min="1" value="20191902" label="Minimum cluster extent used in output"/> + <param name="min_insert" type="integer" min="0" value="0" label="Mean fragment length to use in estimating the unobserved junction rate" /> + <param name="max_coverage" type="integer" min="0" value="500" label="Ignore regions with more than this coverage" /> + <param name="kmer_size" type="integer" min="0" value="24" label="Kmer size" /> + <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for + multiple enzymes" /> + <param name="output_table" type="boolean" truevalue="true" falsevalue="" checked="false" label="Save the collected per-read statistics table to a file" /> + <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose output" /> + </inputs> + + <outputs> + <data name="report" format="json" label="{tool.name} on ${on_string} Report" from_work_dir="out/report.jsonl"/> + <data name="table" format="tabular" label="{tool.name} on ${on_string} Table" from_work_dir="out/table.tsv"/> + <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/qc3C.log"/> + </outputs> + + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + + Documentation can be found at `<https://github.com/cerebis/bin3C>`_. + + ]]></help> +</tool>