--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cami_amber_add_length.xml	Sun Aug 25 13:18:28 2024 +0000
@@ -0,0 +1,90 @@
+<tool id="cami_amber_add" name="CAMI AMBER add length column" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Create gold standard file for CAMI AMBER</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+
+        ln -s '${gold_standard_file}' '$gold_standard_file.element_identifier' &&
+        ln -s '${fasta_file}' '$fasta_file.element_identifier' &&
+
+        add_length_column.py 
+        -g '$gold_standard_file.element_identifier'
+        -f '$fasta_file.element_identifier'
+        > gold_standard_file.tsv
+    ]]>
+    </command>
+    <inputs>
+        <param argument="--gold_standard_file" type="data" format="tabular"
+            label="Input gold standard file here"
+            help="Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!" />
+        <param argument="--fasta_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz"
+            label="Input fasta/fastq file here"
+            help="Input the file which match to the gold standard file" />
+    </inputs>
+    <outputs>
+        <data name="file" format="tabular" from_work_dir="gold_standard_file.tsv" label="${tool.name}: Gold standard file" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="gold_standard_file" value="test_add.tsv" ftype="tabular" />
+            <param name="fasta_file" value="test_add.fasta.gz" ftype="fasta.gz" />
+            <output name="file" >
+                <assert_contents>
+                    <has_size value="124000" delta="3000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+        .. class:: infomark
+
+        **What it does**
+
+        This tool can create the gold standard file which has to be used for the CAMI AMBER. 
+
+        **Input**
+
+        This tool required 2 inputs:
+
+        - A binning file (biobox format)
+
+        This file can be created via the convert_to_biobox tool
+
+        .. class:: infomark
+
+        Example(tab separated):
+
+        ::
+
+         #CAMI Format for Binning
+         @Version:0.9.0
+         @SampleID:CAMI_low
+         @@SEQUENCEID	BINID
+         RL|S1|C10	Bin_034
+         RL|S1|C100	Bin_023
+         RL|S1|C1000	Bin_034
+         RL|S1|C10000	Bin_019
+         RL|S1|C10002	Bin_035
+         RL|S1|C10004	Bin_035
+         RL|S1|C10008	Bin_034
+         RL|S1|C10011	Bin_035
+         RL|S1|C10012	Bin_013
+         RL|S1|C10014	Bin_035
+
+        - A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format)
+
+        This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER
+
+        **Output**
+
+        As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example!
+
+
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>