comparison gtf2featureAnnotation.xml @ 7:14b3f2a4523b draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"

6:1a642de6db01

<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy6" profile="18.01">
    <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" version="2.50.2">bioconductor-biostrings</requirement>
      <requirement type="package" version="1.6.4">r-optparse</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       ln -s '$gtf_input' input.gtf;
       $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf
#if $noheader
--no-header
#end if
#if $version_transcripts
--version-transcripts
#end if
#if $mito.mark_mito
--mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}"
#end if
#if $cdnas.filter_cdnas
--filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}"
#end if
--feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"
	    ]]></command>

    <inputs>

        <param name="feature_type" type="text" optional='true' value="gene" label="Feature type for which to derive annotation"/>
        <param name="first_field" type="text" optional='true' value="gene_id" label="Field to place first in output table"/>
        <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/>
        <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/>
        <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/>
        <conditional name="mito">
          <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/>
          <when value="true">
            <param name="mito_chr" type="text" optional='true' value="mt,mitochondrion_genome,mito,m,chrM,chrMt" label="Comma-separated list of possible mitochondrial chromosome names (case insensitive)"/>
            <param name="mito_biotypes" type="text" optional='true' value="mt_trna,mt_rrna,mt_trna_pseudogene" label="Comma-separated list of possible mitochondrial biotypes (case insensitive)"/>
          </when>
          <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>

    <help><![CDATA[
.. class:: infomark

**What it does**

Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged.

You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).


**Inputs**

    * Ensembl GTF file

title = {Hinxton Single Cell Anlysis Environment},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
  }</citation>
</citations>
</tool>

7:14b3f2a4523b

<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.52.0+galaxy0" profile="18.01">
    <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
    <requirements>
      <requirement type="package" version="1.0.1">atlas-gene-annotation-manipulation</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       ln -s '$gtf_input' input.gtf;
       gtf2featureAnnotation.R --gtf-file input.gtf
#if $noheader
--no-header
#end if
#if $version_transcripts
--version-transcripts
#end if
#if $mito.mark_mito
--mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}"
#end if
#if $cdnas.parse_cdnas
--parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" 
#if $cdnas.filter_cdnas
--filter-cdnas-output "${fasta_output}"
#end if
#if $cdnas.parse_cdna_names
--parse-cdna-names
#end if
#if $fill_empty
--fill-empty "${fill_empty}"
#end if
#end if
--feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"
	    ]]></command>

    <inputs>

        <param name="feature_type" type="text" optional='true' value="gene" label="Feature type for which to derive annotation"/>
        <param name="first_field" type="text" optional='true' value="gene_id" label="Field to place first in output table"/>
        <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/>
        <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/>
        <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/>
        <param name="fill_empty" type="text" optional='true' value="" label="Column to be used to fill empty values in other fields" help="Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping."/>
        <conditional name="mito">
          <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/>
          <when value="true">
            <param name="mito_chr" type="text" optional='true' value="mt,mitochondrion_genome,mito,m,chrM,chrMt" label="Comma-separated list of possible mitochondrial chromosome names (case insensitive)"/>
            <param name="mito_biotypes" type="text" optional='true' value="mt_trna,mt_rrna,mt_trna_pseudogene" label="Comma-separated list of possible mitochondrial biotypes (case insensitive)"/>
          </when>
          <when value="false" />
        </conditional>
        <conditional name="cdnas">
          <param name="parse_cdnas" type="boolean" checked="false" label="Provide a cDNA file for extracting annotations and/ or possible filtering?" 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 in GTF to match with sequences."/>
            <param name="parse_cdna_names" type="boolean" checked="false" label="Parse the FASTA headers for annotation info?" help="e.g. to find gene IDs for transcripts not present in the GTF. May only work for Ensembl GTFs."/>
            <param name="filter_cdnas" type="boolean" checked="false" label="Filter the cDNA file to match the annotations?" />
          </when>
          <when value="false" />
        </conditional>
    </inputs>

    <help><![CDATA[
.. class:: infomark

**What it does**

Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.

You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).


**Inputs**

    * Ensembl GTF file

title = {Hinxton Single Cell Anlysis Environment},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
  }</citation>
  <citation type="doi">10.1101/2020.04.08.032698</citation>
</citations>
</tool>