tools-iuc/data_managers/data_manager_deacon/data_manager/deacon_datamanager.xml at 6c66baf7c5919f6824e4266c6048ef807569678b · galaxyproject/tools-iuc · GitHub

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<tool id="deacon_build_database" name="Deacon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <!-- on update run a local test setting `test` to something else than "true" -->
        <token name="@TOOL_VERSION@">0.12.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">26.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">deacon</requirement>
        <requirement type="package" version="1.6.1">zenodo_get</requirement>
        <requirement type="package" version="1.25.0">wget</requirement>
        <requirement type="package" version="8.21.0">curl</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path' &&
        #if $test != "true"
            #if $input.is_select == "prebuilt"
                #if $download == "human"
                    zenodo_get 17288185 -m -g "*.idx" -o '$out_file.extra_files_path' &&
                #else
                    zenodo_get 17699167 -m -g "*.idx" -o '$out_file.extra_files_path' &&
                #end if
            #else if $input.is_select == "url"
                if curl -sfI "$link" >&2; then
                    wget -P '$out_file.extra_files_path' '$link';
                else
                    echo "Remote file does not exist" >&2 ;
                    exit 1 ;
                fi &&
            #else
                if curl -sfI "$link" >&2; then
                    wget -P '$out_file.extra_files_path' '$link' ;
                    deacon index build '${link.split('/')[-1]}' -o '${file_name}.idx' ;
                    mv '${file_name}.idx' '$out_file.extra_files_path' ;
                else
                    echo "Remote file does not exist" >&2 ;
                    exit 1 ;
                fi &&
            #end if
        #else
            touch '$out_file.extra_files_path'/test.idx &&
        #end if
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import datetime
#set time=datetime.now().strftime("%Y-%m-%d")
{
  "data_tables":{
    "deacon":[
      {
        #if $input.is_select == "prebuilt"
            #if $download == "human"
                "path":"panhuman-1.k31w15.idx",
            #else
                "path":"panmouse-1.k31w15.idx",
            #end if
        #else if $input.is_select == "url"
            "path":"${link.split('/')[-1]}",
        #else
            "path":"${file_name}.idx",
        #end if
            "dbkey":"",
        #if $input.is_select == "prebuilt"
            #if $download == "human"
                "name":"panhuman-1 (k=31, w=15)",
            #else
                "name":"panmouse-1 (k=31, w=15, e=0.5)",
            #end if
        #else
            "name":"$name",
        #end if
        #if $input.is_select == "prebuilt"
            "version":"@TOOL_VERSION@",
        #else
            "version":"$version",
        #end if
        #if $input.is_select == "prebuilt"
            "value":"prebuilt-${time}",
        #else
            "value":"custom-${time}",
        #end if
        "format_version":"3",
        #if $input.is_select == "prebuilt"
            "note":"Prebuilt index files from the devs of deacon"
        #else
            "note":"$note"
        #end if
      }
    ]
  }
}]]>
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="input">
            <param name="is_select" type="select" label="Choose how to add data to the DM">
                <option value="url">Copy an index file from an URL</option>
                <option value="prebuilt" selected="true">Download a prebuilt file</option>
                <option value="fasta">Download a fasta file and build index file from it</option>
            </param>
            <when value="prebuilt">
                <param name="download" type="select" label="Select which prebuilt should be downloaded" help="See help section for more information">
                    <option value="human">panhuman-1 (k=31, w=15)</option>
                    <option value="mouse">panmouse-1 (k=31, w=15, e=0.5)</option>
                </param>
            </when>
            <when value="url">
                <param name="link" type="text" label="Input the URL to download a index file"/>
                <param name="name" type="text" label="Set the name for the entry in the DM" help="For an example look in the name of the prebuilt files. Also add in brackets the values used for building the file!"/>
                <param name="version" type="text" label="Which version was used to build the file to copy" help="State the tool version used to build the index file"/>
                <param name="note" type="text" label="Add a note" help="Here some notes can be set for example from where the data comes, who created the data and so on"/>
            </when>
            <when value="fasta">
                <param name="file_name" type="text" label="Enter filename" help="Please enter the name of the file which will be downloaded without the extension" />
                <param name="link" type="text" label="Input the URL to download a fasta file for using it to build an index file"/>
                <param name="name" type="text" label="Set the name for the entry in the DM" help="For an example look in the name of the prebuilt files. Also add in brackets the values used for building the file!"/>
                <param name="version" type="text" label="Which version was used to build the file to copy" help="State the tool version used to build the index file"/>
                <param name="note" type="text" label="Add a note" help="Here some notes can be set for example from where the data comes, who created the data and so on"/>
            </when>
        </conditional>
        <param name="test" type="hidden"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="is_select" value="prebuilt"/>
                <param name="download" value="human"/>
            </conditional>
            <param name="test" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"format_version":"3"'/>
                    <has_text text='"name":"panhuman-1 (k=31, w=15)"'/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="is_select" value="url"/>
                <param name="link" value="https://zenodo.org/records/17288185/files/panhuman-1.k31w15.idx"/>
                <param name="name" value="panhuman-1 (k=31, w=15)"/>
                <param name="version" value="0.12.0"/>
                <param name="note" value="test"/>
            </conditional>
            <param name="test" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"format_version":"3"'/>
                    <has_text text='"name":"panhuman-1 (k=31, w=15)"'/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="is_select" value="fasta"/>
                <param name="file_name" value="panhuman-1.k31w15_test"/>
                <param name="link" value="https://zenodo.org/records/17288185/files/panhuman-1.k31w15.fasta"/>
                <param name="name" value="panhuman-1 (k=31, w=15)"/>
                <param name="version" value="0.12.0"/>
                <param name="note" value="test"/>
            </conditional>
            <param name="test" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text='"format_version":"3"'/>
                    <has_text text='"name":"panhuman-1 (k=31, w=15)"'/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="1" expect_failure="true">
            <conditional name="input">
                <param name="is_select" value="fasta"/>
                <param name="file_name" value="panhuman-1.k31w15_test"/>
                <param name="link" value="https://zenodo.org/records/17288185/files/panhuman-1.k31w15adasdasd.fasta"/>
                <param name="name" value="panhuman-1 (k=31, w=15)"/>
                <param name="version" value="0.12.0"/>
                <param name="note" value="test"/>
            </conditional>
            <param name="test" value="false"/>
            <assert_stderr>
                <has_text text="Remote file does not exist"/>
            </assert_stderr>
        </test>
        <test expect_exit_code="1" expect_failure="true">
            <conditional name="input">
                <param name="is_select" value="url"/>
                <param name="link" value="https://zenodo.org/records/17288185/files/panhuman-1.k31w15adasdasd.fasta"/>
                <param name="name" value="panhuman-1 (k=31, w=15)"/>
                <param name="version" value="0.12.0"/>
                <param name="note" value="test"/>
            </conditional>
            <param name="test" value="false"/>
            <assert_stderr>
                <has_text text="Remote file does not exist"/>
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
Download prebuilt index files for deacon or download other index files made for deacon via url.
    ]]></help>
    <citations>
        <citation type="doi">10.1101/2025.06.09.658732</citation>
    </citations>
</tool>