Mercurial > repos > thanhlv > bin3c
changeset 0:eb31dd5dc3ed draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
| author | thanhlv |
|---|---|
| date | Thu, 26 Sep 2019 12:12:13 -0400 |
| parents | |
| children | 15d48ce4e275 |
| files | cluster.xml macros.xml mkmap.xml |
| diffstat | 3 files changed, 136 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster.xml Thu Sep 26 12:12:13 2019 -0400 @@ -0,0 +1,56 @@ +<tool id="cluster" name="cluster" version="@VERSION@"> + <description>Cluster an existing contact map into genome bins</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + bin3C cluster + $clobber + --max-image $max_image + --min-extent $min_extent + --min-reflen $min_reflen + --min-signal $min_signal + -s 201987356473 + $no_report + $no_spades + $no_plot + $no_fasta + $only_large + $fasta + $contact_map out + ]]></command> + + <inputs> + <param name="contact_map" type="data" format="gz" label="Contact map" help="This file is generated from mkmap command" /> + <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" label="Clobber existing files" /> + <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/> + <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/> + <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/> + <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/> + <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" /> + <param name="no_spades" type="boolean" truevalue="--no-spades" falsevalue="" checked="false" label="Assembly was not done using SPAdes" /> + <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" /> + <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" /> + <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" /> + <param name="fasta" type="data" format="fasta" label="Alternative source FASTA location from that supplied during mkmap" /> + </inputs> + + <outputs> + <data name="output" label="${tool.name} on ${on_string} Output"> + <discover_datasets pattern="__designation_and_ext__" directory="out" /> + </data> + </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/macros.xml Thu Sep 26 12:12:13 2019 -0400 @@ -0,0 +1,17 @@ +<macros> + <token name="@VERSION@">0.3</token> + <xml name="requirements"> + <requirements> + <container type="singularity">path/to/bin3c.sif</container> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>bin3C -V | grep -E -o "([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/mkmap.xml Thu Sep 26 12:12:13 2019 -0400 @@ -0,0 +1,63 @@ +<tool id="mkmap" name="mkmap" version="@VERSION@"> + <description>Create a new contact map from assembly sequences and Hi-C bam file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + bin3C mkmap + $clobber + --max-image $max_image + --min-extent $min_extent + --min-reflen $min_reflen + --min-signal $min_signal + $eta + #if bin_size != 0 + --bin-size $bin_size + #end if + #if min_insert != 0 + --min-insert $min_insert + #end if + --min-mapq $min_mapq + --strong $strong + #if neb_name != "" + --enzyme $neb_name + #end if + $ref $bam out + ]]></command> + + <inputs> + <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" /> + <param name="bam" type="data" format="bam" label="Input bam file in query order" /> + <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" label="Clobber existing files" /> + <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/> + <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/> + <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/> + <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/> + <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" /> + <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" /> + <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" /> + <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" /> + <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" /> + <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for + multiple enzymes" /> + </inputs> + + <outputs> + <data name="output" label="${tool.name} on ${on_string} Output"> + <discover_datasets pattern="__designation_and_ext__" directory="out" /> + </data> + </outputs> + + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + + Documentation can be found at `<https://github.com/cerebis/bin3C>`_. + + ]]></help> +<expand macro="citations" /> +</tool>