# HG changeset patch
# User iuc
# Date 1717501301 0
# Node ID afc795d1091899bdee292655b3748a58dd4c53f9
# Parent  6c71acde9d52919b94c0fc2b2792e4334208f356
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit eec9d5fede4b4b81bd163e00a1654bd33c589fb3

diff -r 6c71acde9d52 -r afc795d10918 cami_amber_add_length.xml
--- a/cami_amber_add_length.xml	Mon May 20 18:08:36 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<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>
diff -r 6c71acde9d52 -r afc795d10918 cami_amber_convert_to_biobox.xml
--- a/cami_amber_convert_to_biobox.xml	Mon May 20 18:08:36 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,162 +0,0 @@
-<tool id="cami_amber_convert" name="CAMI AMBER convert to biobox" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>Create binning file(s) for CAMI AMBER</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code">
-    <![CDATA[
-
-    mkdir -p output 
-
-    #for $file in $input.files:
-        &&
-        ln -s '$file' './$file.element_identifier' 
-    #end for
-
-    #if $work == "single":
-        #for $file in $input.files:
-            &&
-            #set $out = $file.element_identifier.split('.')[0] + '.tsv'
-            convert_fasta_bins_to_biobox_format.py
-            -o 'output/$out'
-            '$file.element_identifier'
-        #end for
-    #else:
-        &&
-        convert_fasta_bins_to_biobox_format.py
-        -o 'output/binning.tsv'
-        #for $file in $input.files:
-            '$file.element_identifier'
-        #end for
-    #end if
-
-    ]]>
-    </command>
-    <inputs>
-        <param name="work" type="select" label="Merge binning output files?"
-            help="If yes all input files will be merged into one biobox output (required input by amber). If no each input will be converted into a separate biobox output file." >
-            <option value="single">Each file alone</option>
-            <option value="all">All together</option>
-        </param>
-        <conditional name="input">
-            <param name="is_select" type="select" label="Choose how to input the files"
-                help="You can provide each input separately or as a collection">
-                <option value="manually">Manually</option>
-                <option value="data">Data collection</option>
-            </param>
-            <when value="manually">
-                <param name="files" type="data" format="fasta" multiple="true"
-                    label="Input fasta files"
-                    help="Input all fasta files which this tool should convert into biobox format" />
-            </when>
-            <when value="data">
-                <param name="files" type="data_collection" collection_type="list" format="fasta"
-                    label="Input the fasta collection"
-                    help="Input the fasta collected which the tool should convert into biobox format" />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="binning_file" format="tabular" from_work_dir="output/binning.tsv" label="${tool.name}: BINNING FILE">
-            <filter>work and "all" in work</filter>
-        </data>
-        <collection name="binning_collection" type="list" label="${tool.name}: BINNING COLLECTION" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" format="tabular" directory="output/" recurse="true" />
-            <filter>work and "single" in work</filter>
-        </collection>
-    </outputs>
-    <tests>
-        <test expect_num_outputs="1" >
-            <param name="work" value="single" />
-            <conditional name="input" >
-                <param name="is_select" value="manually" />
-                <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" />
-            </conditional>
-            <output_collection name="binning_collection" type="list">
-                <element name="test_add1" >
-                    <assert_contents>
-                        <has_n_lines n="1464" />
-                    </assert_contents>
-                </element>
-                <element name="test_add2" >
-                    <assert_contents>
-                        <has_n_lines n="36" />
-                    </assert_contents>
-                </element>
-            </output_collection>
-        </test>
-        <test expect_num_outputs="1" >
-            <param name="work" value="single" />
-            <conditional name="input" >
-                <param name="is_select" value="data" />
-                <param name="files" >
-                    <collection name="test" type="list" >
-                        <element name="test_add1" value="test_add1.fasta" />
-                        <element name="test_add2" value="test_add2.fasta" />
-                    </collection>
-                </param>
-            </conditional>
-            <output_collection name="binning_collection" type="list">
-                <element name="test_add1" >
-                    <assert_contents>
-                        <has_n_lines n="1464" />
-                    </assert_contents>
-                </element>
-                <element name="test_add2" >
-                    <assert_contents>
-                        <has_n_lines n="36" />
-                    </assert_contents>
-                </element>
-            </output_collection>
-        </test>
-        <test expect_num_outputs="1" >
-            <param name="work" value="all" />
-            <conditional name="input" >
-                <param name="is_select" value="manually" />
-                <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" />
-            </conditional>
-            <output name="binning_file">
-                <assert_contents>
-                    <has_n_lines n="1496" />
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="1" >
-            <param name="work" value="all" />
-            <conditional name="input" >
-                <param name="is_select" value="data" />
-                <param name="files" >
-                    <collection name="test" type="list" >
-                        <element name="test_add1" value="test_add1.fasta" />
-                        <element name="test_add2" value="test_add2.fasta" />
-                    </collection>
-                </param>
-            </conditional>
-            <output name="binning_file">
-                <assert_contents>
-                    <has_n_lines n="1496" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help>
-    <![CDATA[
-        .. class:: infomark
-
-        **What it does**
-
-        This tool can create a tsv file in biobox format or a collection of multiple files.
-
-        **Input**
-
-        This tool required only fasta files. You can submit n files manually or a collection of fasta files.
-
-        **Output**
-
-        This tool either give out 1 binning file in biobox format or for each inputted file 1 binning file in biobox format.
-
-    ]]>
-    </help>
-    <expand macro="citations" />
-</tool>