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<tool id="ctat_lncrna" name="ctat_lncrna" version="1.0.0" profile="17.05">

    <description>Filters a high-quality set of lncRNA from reconstructed RNA-seq data</description>
    <requirements>
    <requirement type="package" version="1.0.1">ctat-lncrna</requirement>
    </requirements>
    <command detect_errors="default">
      <![CDATA[
     #if str($bedfile) != "":
     lncrna --bedfile $bedfile
     --config "${assembly.fields.path}" 
     #end if

     #if str($assembly) != "":
         --assembly "${assembly.fields.value}"
     #end if

     #if $min_overlap != "":
         --min_overlap "$min_overlap"
     #end if

     #if str($min_cluster) != "":
         --min_cluster "$min_cluster"
     #end if

     #if str($min_coding) != "":
         --min_coding "$min_coding"
     #end if

    #if str($minMatch) != "":
        --minMatch "$minMatch"
    #end if

    #if str($pad) != "":
        --pad "$pad"
    #end if

    #if str($gap_open) != "":
        --gap_open "$gap_open"
    #end if

    #if str($gap_extend) != "":
        --gap_extend "$gap_extend"
    #end if
    --web 
    && cp -r slncky.EvolutionBrowser $html_file.files_path
]]>
    </command>

    <inputs>
      <param name="bedfile" format="interval" type="data" value="bedfile" label="Bed File:" help="Reconstructed transcripts (ex. from StringTie or Trinity)"/>
      <param name="min_overlap" type="float" value="0.0" label="Min overlap" help="Remove any transcript that overlap annotated coding gene greater than min_overlap" />
      <param name="min_cluster" type="integer" value="2" label="Min cluster" help="Minimum size of duplication clusters to remove" />
      <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/>
      <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" />
      <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" />
      <param name="gap_open" type="integer" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/>
      <param name="gap_extend" type="integer" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/>
      <param name="assembly" type="select" label="Choose annotation:" help="Select annotation">
            <options from_data_table="ctat_lncrna_annotations" />
      </param>
    </inputs>

    <outputs>
           <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/>
           <data format="tabular" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/>
           <data format="tabular" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/>
           <data format="tabular" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/>
           <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/>
           <data format="tabular" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/>
           <data format="tabular" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/>
           <data format="tabular" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/>
           <data format="tabular" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/>
    </outputs>

    <stdio>
          <exit_code range="1:" level="fatal" description="Error in SLNCky" />
    </stdio>

    <tests>
        <test>
            <param name="bedfile" value="reads.simPE.StringTie.transcripts.bed" />
            <param name="assembly" value="hg19" /> 
            <param name="min_overlap" value="0.0" />
            <param name="min_cluster" value="2" />
            <param name="min_coding" value="0.1" />
            <param name="minMatch" value="0.1" />
            <param name="pad" value="0" />
            <param name="gap_open" value="200" />
            <param name="gap_extend" value="40" />

            <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
            <output name="html_file" file="slncky/reads.simPE.browse.html" />

            <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
            <output name="canonical_to_lncs" file="slncky/reads.simPE.canonical_to_lncs.txt" />
 
            <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
            <output name="cluster_info" file="slncky/reads.simPE.cluster_info.txt" />

            <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
            <output name="filtered_info" file="slncky/reads.simPE.filtered_info.txt" />

            <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
            <output name="lncs" file="slncky/reads.simPE.lncs.bed" />

            <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
            <output name="lncs_info" file="slncky/reads.simPE.lncs.info.txt" />

            <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
            <output name="orfs" file="slncky/reads.simPE.orfs.txt" />

            <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
            <output name="orthologs_top" file="slncky/reads.simPE.orthologs.top.txt" />

            <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
            <output name="orthologs" file="slncky/reads.simPE.orthologs.txt" />

        </test>
        <test>
            <param name="bedfile" value="mir-17-92.StringTie.transcripts.bed" />
            <param name="assembly" value="hg19" /> 
            <param name="min_overlap" value="0.0" />
            <param name="min_cluster" value="2" />
            <param name="min_coding" value="0.1" />
            <param name="minMatch" value="0.1" />
            <param name="pad" value="0" />
            <param name="gap_open" value="200" />
            <param name="gap_extend" value="40" />

            <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
            <output name="html_file" file="slncky/mir-17-92.browse.html" />

            <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
            <output name="canonical_to_lncs" file="slncky/mir-17-92.canonical_to_lncs.txt.sorted" sort="true" />
 
            <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
            <!-- This file isn't being created for some reason...
            <output name="cluster_info" >
                <assert_contents>
                    <has_line_matching expression=".+" />
                </assert_contents>
            </output>
            -->

            <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
            <output name="filtered_info" file="slncky/mir-17-92.filtered_info.txt.sorted" sort="true" />

            <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
            <output name="lncs" file="slncky/mir-17-92.lncs.bed" />

            <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
            <output name="lncs_info" file="slncky/mir-17-92.lncs.info.txt" />

            <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
            <output name="orfs" file="slncky/mir-17-92.orfs.txt" />

            <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
            <output name="orthologs_top" file="slncky/mir-17-92.orthologs.top.txt" />

            <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
            <output name="orthologs" file="slncky/mir-17-92.orthologs.txt" />
        </test>
    </tests>

    <help>
.. class:: infomark

slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.

To learn more about slncky visit their website_ .

.. _website: https://github.com/slncky/slncky

</help>

<citations>
        <citation type="doi">10.1186/s13059-016-0880-9</citation>
</citations>

</tool>