diff biobox_add_taxid.xml @ 0:1e10251b9615 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biobox_add_taxid.xml	Sun Aug 25 13:19:14 2024 +0000
@@ -0,0 +1,119 @@
+<tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Add taxid output from BAT or GTDB to biobox binning data</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@SCRIPT_VERSION@">0.4</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+
+        mkdir -p input &&
+
+        ln -s '${biobox_file}' '$biobox_file.element_identifier' &&
+
+        #for $i, $f in enumerate($tool_type.input):
+            ln -s '$f' 'input/${i}.tsv' &&
+        #end for
+
+        biobox_add_taxid.py
+        '$biobox_file.element_identifier'
+        '$tool_type.is_select'
+        'input'
+        #if $tool_type.is_select == 'GTDB':
+            -g '$gtdb_to_taxdump'
+            -t '$taxonkit'
+            -c $column
+        #end if
+        &&
+
+        #if $tool_type.is_select == 'GTDB':
+            cp *_add_taxid_GTDB* $output
+        #else:
+            cp *_add_taxid_BAT* $output
+        #end if
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="biobox_file" type="data" format="tabular" label="CAMI amber biobox file input" help="Input the CAMI amber biobox file here which are corespond with the biner and the BAT/GTDB output which did used the biner as input! "/>
+        <conditional name="tool_type">
+            <param name="is_select" type="select" label="Select the tool which output should be used here" help="Select BAT when you use the bin2classifier file(s) or select GTDB when using the summary file(s)">
+                <option value="BAT">BAT</option>
+                <option value="GTDB">GTDB</option>
+            </param>
+            <when value="GTDB">
+                <param argument="--gtdb_to_taxdump" type="data" format="tabular" label="Input the output from gtdb_to_taxdump here" help="Use the output from gtdb_to_taxdump here since we need the mapped names from GTDB to NCBI to get the arcoding taxids from NCBI"/>
+                <param argument="--taxonkit" type="data" format="tabular" label="Input the output from Taxonkit here" help="Use the output from Taxonkit here since the need the mapped NCBI names to the arcording taxids"/>
+                <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/>
+                <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here"
+                    help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/>
+            </when>
+            <when value="BAT">
+                <param name="input" type="data" multiple="true" format="tabular" label="Input bin2classifier file(s) from BAT here"
+                    help="Use the BAT file(s) which are coresponding with the binning file!"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name}: BIOBOX ADD TAXID COLUMN"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
+            <conditional name="tool_type">
+                <param name="is_select" value="BAT"/>
+                <param name="input" ftype="tabular" value="test_bat_file.tsv"/>
+            </conditional>
+            <output name="output" file="test_biobox_file_add_taxid_bat.tsv"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
+            <conditional name="tool_type">
+                <param name="is_select" value="GTDB"/>
+                <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/>
+                <param name="taxonkit" ftype="tabular" value="test_taxonkit_file.tsv"/>
+                <param name="column" value="1"/>
+                <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/>
+            </conditional>
+            <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+        
+        **USAGE OF THIS TOOL**
+
+        This tool was desgin for using the BAT/GTDB-Tk output to expand the CAMI amber biobox file with the taxid column to access taxa evaluation with amber!
+
+        **IMPORTAND NOTE WHEN USING GTDB OUTPUT**
+
+        Befor using GTDB-Tk output you have to use 2 other tools to map the GTDB names to the NCBI names and then map the NCBI names to there taxids.
+        To map the GTDB names to the NCBI names you extract the GTDB names from the summary file and with them you can now use the gtdb_to_taxdum tool!
+        After using the gtdb_to_taxdum tool you have the extract the NCBI names here and then use the tool Taxonkit[name2taxid] to finaly get the taxids.
+
+        **INPUTS**
+        - The CAMI amber biobox file
+        - BAT[bin2classifier] file(s) OR GTDB-Tk[Summary] file(s)
+        - The gtdb_to_taxdum output[WHEN USING GTDB-Tk]
+        - The Taxonkit[name2taxid] output[WHEN USING GTDB-Tk]
+
+        **OUTPUT**
+
+        A CAMI amber biobox file with a taxid colum
+    ]]> 
+    </help>
+    <citations>
+        <citation type="bibtex">@misc{BibEntry2024Aug,
+            title = {{biobox{$\_$}add{$\_$}taxid}},
+            author = {Santino Faack (SantaMcCloud)},
+            journal = {GitHub},
+            year = {2024},
+            month = aug,
+            note = {[Online; accessed 22. Aug. 2024]},
+            url = {https://github.com/SantaMcCloud/biobox_add_taxid/tree/release-0.3}
+        }</citation>
+    </citations>
+</tool>