comparison instagraal.xml @ 2:d1be552c6034 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/instagraal commit c5ff906bec1f07b06a60081f7db3fc8f0c6e94b8

1:8d5b13b571fd

<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Large genome reassembly based on Hi-C data</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">instagraal</xref>
    </xrefs>
    <stdio>
        <regex match="instagraal_class" level="warning" description="instaGRAAL is raining an expected error at the end."/>
        <regex match="Exception:"/>
        <exit_code range="2:"/>
        <exit_code range=":-1"/>
    </stdio>
    <requirements>
        <container type="docker">koszullab/instagraal</container>
    </requirements>
    <version_command>instagraal --version</version_command>
    <command>
    <![CDATA[

#set gap_string = 'N' * int($number_of_n)

        <param argument="--coverage-std" type="integer" value="1" min="0" max="1" label="Number of standard deviations below the mean"
            help="Coverage below which fragments should be filtered out prior to binning." />

        <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" />
        <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" />
        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Indicates genome is circular" />
        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" />
        <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" />
        <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" />
        <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step" />

    </inputs>
    <outputs>
        <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta"/>
        <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt"/>
        <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
            <param name="fragments_list" value="fragments_list.tabular" />

2:d1be552c6034

<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>Large genome reassembly based on Hi-C data</description>
    <xrefs>
        <xref type="bio.tools">instagraal</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">0.1.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <!-- use a versioned copy of the upstream container at koszullab/instagraal -->
        <container type="docker">quay.io/galaxy/instagraal:0.1.6</container>
        <resource type="cuda_version_min">10.0</resource>
        <resource type="cuda_compute_capability">3.0</resource>
        <resource type="cuda_device_count_min">1</resource>
    </requirements>
    <stdio>
        <regex match="instagraal_class" level="warning" description="instaGRAAL is raining an expected error at the end."/>
        <regex match="Exception:"/>
        <exit_code range="2:"/>
        <exit_code range=":-1"/>
    </stdio>
    <version_command>instagraal --version</version_command>
    <command>
    <![CDATA[

#set gap_string = 'N' * int($number_of_n)

        <param argument="--coverage-std" type="integer" value="1" min="0" max="1" label="Number of standard deviations below the mean"
            help="Coverage below which fragments should be filtered out prior to binning." />

        <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" />
        <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" />
        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" />
        <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" />
        <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" />
        <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step" />

    </inputs>
    <outputs>
        <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta" label="${tool.name} on ${on_string}: Genome sequence"/>
        <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt" label="${tool.name} on ${on_string}: Fragment information"/>
        <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta" label="${tool.name} on ${on_string}: Curated sequences"/>
    </outputs>
    <tests>
        <test>
            <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
            <param name="fragments_list" value="fragments_list.tabular" />