comparison maxbin2.xml @ 1:864279a0d64b draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit c003bb1aa5c8c42650b27516f0951e0d67f11857-dirty

0:35aa0df55a62

<tool id="maxbin2" name="MaxBin2" version="2.2.4">
    <requirements>
        <requirement type="package" version="2.2.4">maxbin2</requirement>
    </requirements>
    <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

                  <option value="rds" selected="true">Sequencing Reads</option>
                  <option value="abdc">Abundances</option>
              </param>
              <when value="rds">
                  <param name="reads" argument="-read/-read2/..." type="data" format="fasta,fastq" multiple="true" label="Reads file(s)"/>
                  <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file if you were to use this option." />
              </when>
              <when value="abdc">
                  <param name="abund" argument="-abund/-abund2/..." type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
              </when>
          </conditional>

            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
        </collection>
        <!-- additional output in case of reassembly -->
	<collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
            <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
        </collection>
        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
            <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
        </collection>
        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
        </data>
        <data name="reassembly_n50" format="text" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test w contigs and reads as input -->
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />

            <output_collection name="reassembly_reads" type="list" count="2">
                <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
                <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
            </output_collection>
            <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
            <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="text" />
        </test>
    </tests>
    <help><![CDATA[
MaxBin is a software that clusters metagenomic contigs into different bins,
each consists (hopefully) of contigs from one species. MaxBin uses the

1:864279a0d64b

<tool id="maxbin2" name="MaxBin2" version="2.2.4_galaxy1">
    <requirements>
        <requirement type="package" version="2.2.4">maxbin2</requirement>
    </requirements>
    <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

                  <option value="rds" selected="true">Sequencing Reads</option>
                  <option value="abdc">Abundances</option>
              </param>
              <when value="rds">
                  <param name="reads" argument="-read/-read2/..." type="data" format="fasta,fastq" multiple="true" label="Reads file(s)"/>
                  <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
              </when>
              <when value="abdc">
                  <param name="abund" argument="-abund/-abund2/..." type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
              </when>
          </conditional>

            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
        </collection>
        <!-- additional output in case of reassembly -->
	<collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
            <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </collection>
        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
            <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </collection>
        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test w contigs and reads as input -->
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />

            <output_collection name="reassembly_reads" type="list" count="2">
                <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
                <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
            </output_collection>
            <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
            <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" />
        </test>
    </tests>
    <help><![CDATA[
MaxBin is a software that clusters metagenomic contigs into different bins,
each consists (hopefully) of contigs from one species. MaxBin uses the