comparison id_converter.xml @ 7:59da262c572c draft

planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty

6:c1364679388d

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$idto.idtypeout"
        --output="$output"
        --ref_file="$__tool_directory__/tool-data/human_id_mapping_file.txt"
        
    </command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >

                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
            </when>
        </conditional>
	    <conditional name="idti" >
            <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
		        <option value="neXtProt_ID" >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>

.. class:: infomark

This tool converts human IDs using the following source files:

* HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
    Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

* nextprot_ac_list_all.txt (Nextprot released on 01/08/2017)
    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/

-----

.. class:: warningmark

7:59da262c572c

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$idto.idtypeout"
        --output="$output"
        --ref_file="$human_id_mapping"
        
    </command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >

                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
            </when>
        </conditional>
        <param name="human_id_mapping" type="select" label="Select species for ID conversion" >
            <options from_file="human_id_mapping.loc" >
                <column name="name" index="1" />
                <column name="value" index="2" />
            </options>
        </param>
	    <conditional name="idti" >
            <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
		        <option value="neXtProt_ID" >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>

.. class:: infomark

This tool converts human IDs using the following source files:

* HUMAN_9606_idmapping_selected.tab (Uniprot 15/05/2018)
    Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

* nextprot_ac_list_all.txt (Nextprot released on 17/01/2018)
    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/

-----

.. class:: warningmark