comparison id_converter.xml @ 16:b6607b7e683f draft

planemo upload commit f2b3d1ff6bea930b2ce32c009e4d3de39a17edfb-dirty

15:b50d913ec067

<tool id="IDconverter" name="ID Converter" version="2018.12.18">
    <description>(Human, Mouse, Rat)
    </description>
    <requirements>
      <requirement type="package" version="3.4.1">R</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript">
        $__tool_directory__/id_converter.R
        --id_type="$species.idtypein"
        #if $input.ids == "text"
            --input="$input.txt"
            --input_type="list"
        #else

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$species.idto.idtypeout"
        --output="$output"
        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }"
        
    </command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >
                <option value="text">Copy/paste your identifiers</option>
                <option value="file" selected="true">Input file containing IDs</option>

            </when>
        </conditional>
        <conditional name="species">
            <param name="mapping_file" type="select" label="Species" >
                <options from_data_table="proteore_id_mapping"/>
                <option value="human_id_mapping"></option>
                <option value="mouse_id_mapping"></option>
                <option value="rat_id_mapping"></option>
            </param>
            <when value="human_id_mapping">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>

                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="mouse_id_mapping">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>

                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="rat_id_mapping">
                <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>

16:b6607b7e683f

<tool id="IDconverter" name="ID Converter" version="2019.01.28">
    <description>(Human, Mouse, Rat)
    </description>
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        python $__tool_directory__/id_converter.py 
        --id_type="$species.idtypein"
        #if $input.ids == "text"
            --input="$input.txt"
            --input_type="list"
        #else

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$species.idto.idtypeout"
        --output="$output"
        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[2] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }"
        
    ]]></command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >
                <option value="text">Copy/paste your identifiers</option>
                <option value="file" selected="true">Input file containing IDs</option>

            </when>
        </conditional>
        <conditional name="species">
            <param name="mapping_file" type="select" label="Species" >
                <options from_data_table="proteore_id_mapping"/>
                <option value="Human"></option>
                <option value="Mouse"></option>
                <option value="Rat"></option>
            </param>
            <when value="Human">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>

                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="Mouse">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>

                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="Rat">
                <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>