comparison gtf2featureAnnotation.xml @ 3:b95e6a9bb15c draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552-dirty

2:e255c0e5dfca

<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy2">
    <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
    <requirements>
      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
      <requirement type="package">bioconductor-biostrings</requirement>
      <requirement type="package">r-optparse</requirement>

          <when value="false" />
        </conditional>
        <conditional name="cdnas">
          <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/>
          <when value="true">
            <param name="fasta_input" type="data" format="fasta" label="FASTA-format cDNA/ transcript file" />
            <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/>
          </when>
          <when value="false" />
        </conditional>
    </inputs>

    <outputs>
        <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/>
        <data name="fasta_output" format="fasta" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences">
          <filter>filter_cdnas</filter>
        </data>
    </outputs>
    <tests>
      <test>

3:b95e6a9bb15c

<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy3">
    <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
    <requirements>
      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
      <requirement type="package">bioconductor-biostrings</requirement>
      <requirement type="package">r-optparse</requirement>

          <when value="false" />
        </conditional>
        <conditional name="cdnas">
          <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/>
          <when value="true">
            <param name="fasta_input" type="data" format="fasta,fasta.gz" label="FASTA-format cDNA/ transcript file" />
            <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/>
          </when>
          <when value="false" />
        </conditional>
    </inputs>

    <outputs>
        <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/>
        <data name="fasta_output" format="fasta.gz" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences">
          <filter>filter_cdnas</filter>
        </data>
    </outputs>
    <tests>
      <test>