diff tiara.xml @ 0:3f33a8ac8891 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tiara.xml	Thu May 30 11:10:39 2024 +0000
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+<tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[ 
+        
+        tiara 
+        -t \${GALAXY_SLOTS:-4} 
+        -i '$input' 
+        -o '$output'
+
+        #if $taxonomy_filter
+            --tf #for $tf in $taxonomy_filter
+                $tf
+            #end for
+        #end if   
+        #if $probabilities
+            --pr '$probabilities'
+        #end if
+        #if $min_len
+            -m '$min_len'
+        #end if
+        #if $cutoff_stage1
+            -p $cutoff_stage1
+            #if $cutoff_stage2
+            $cutoff_stage2
+            #end if
+        #end if
+        #if $advanced_options.advance.customize_kmer_length == 'customize'
+            --k1 $advanced_options.advance.first_stage_kmer
+            --k2 $advanced_options.advance.second_stage_kmer
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="input fasta,fasta.gz file"/>
+        <param name="taxonomy_filter" type="select" multiple="true" optional="true" label="Write sequences to fasta,fasta.gz files specified in the arguments to this option." help="all refers to all classes present in input fasta (to separate fasta files).">
+            <option value="mit">mitochondria</option>
+            <option value="pla">plastid</option>
+            <option value="bac">bacteria</option>
+            <option value="arc">archea</option>
+            <option value="euk">eukarya</option>
+            <option value="unk">unknown</option>
+            <option value="pro">prokarya</option>
+            <option value="all">all</option>
+        </param>
+        <param argument="probabilities" type="boolean" truevalue="--pr" falsevalue="" checked="false" label="Add probabilities of individual classes for each sequence."/>
+        <param argument="min_len" type="integer" value="3000" min="1000" optional="true" label="Minimum length of a sequence. Default: 3000 bp." help="Specify the desired minimum length in base pairs.Default value is 3000 bp and we do not recommend classifying sequences shorter than 1000 bp. "/>
+        <param argument="cutoff_stage1" type="float" value="0.65" min="0.5" max="1" optional="true" label="Probability threshold for the first stage." help="Probability threshold needed for classification in the first stage. Default: 0.65." />
+        <param argument="cutoff_stage2" type="float" value="0.65" min="0.5" max="1" optional="true" label="Probability threshold for the second stage." help="Probability threshold needed for classification in the second stage. Default: 0.65." /> 
+        <section name="advanced_options" title="k-mer" expanded="true">
+            <conditional name="advance">
+                <param argument="customize_kmer_length" type="select" label="Advanced options">
+                    <option value="default_options">No, Use param defaults</option>
+                    <option value="customize">Yes, See full parameter list</option>
+                </param>
+                <when value="customize">
+                    <param argument="first_stage_kmer" type="select" label="Select k-mer length used in the first stage of classification (Default: 6).">
+                        <option value="4">k-mer length 4</option>
+                        <option value="5">k-mer length 5</option>
+                        <option value="6" selected="True">default k-mer length</option>
+                    </param>
+                    <param argument="second_stage_kmer" type="select" label="k-mer length used in the second stage of classification (Default: 7).">
+                        <option value="4">k-mer length 4</option>
+                        <option value="5">k-mer length 5</option>
+                        <option value="6">k-mer length 6</option>
+                        <option value="7" selected="True">default k-mer length</option>
+                    </param>
+                </when>
+                <when value="default_options">
+                    <!-- Define actions or defaults for the default option if necessary -->
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} on ${on_string}: sequence ID, classification results"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="plast_fr.fasta.gz"/>
+            <param name="taxonomy_filter" value="pla"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*sequence_id*"/>
+                    <has_n_lines n="11" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="mitplas1.fasta"/>
+            <param name="taxonomy_filter" value="pla,mit"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*sequence_id*"/>
+                    <has_n_lines n="30" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="sample_all.fasta"/>
+            <param name="taxonomy_filter" value="all"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*sequence_id*"/>
+                    <has_n_lines n="51" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="sample_all.fasta"/>
+            <param name="taxonomy_filter" value="euk,bac,arc,unk"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*sequence_id*"/>
+                    <has_n_lines n="51" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="eukarya_fr.fasta"/>
+            <param name="taxonomy_filter" value="euk"/>
+            <param name="min_len" value="5000"/>
+            <param name="cutoff_stage1" value="0.65"/>
+            <param name="cutoff_stage2" value="0.60"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*sequence_id*"/>
+                    <has_n_lines n="11" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="bacteria_fr.fasta"/>
+            <param name="taxonomy_filter" value="bac"/>
+            <param name="min_len" value="5000"/>
+            <param name="cutoff_stage1" value="0.65"/>
+            <param name="cutoff_stage2" value="0.60"/>
+            <param name="probabilities" value="true"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression=".*bac*"/>
+                    <has_n_lines n="11" delta="5"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+Tiara is a Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.
+
+How it works
+============
+The sequences are classified in two stages:
+
+First Stage:
+Input: Sequences are classified into classes: archaea, bacteria, prokarya, eukarya, organelle, and unknown.
+Output: Classifications for each sequence into one of the above classes.
+
+Second Stage:
+Input: Sequences labeled as organelle from the first stage.
+Output: Further classification into mitochondria, plastid, or unknown.
+
+Required Inputs
+===============
+The primary input for Tiara is metagenomic sequence data that needs classification.
+
+Generated Outputs
+=================
+The output will be the sequences categorized into specific classes as described above.
+
+Additional Resources
+====================
+For a more comprehensive understanding of tiara and detailed usage instructions, please visit the tiara GitHub repository:
+tiara GitHub Repository: [https://github.com/ibe-uw/tiara]
+        
+    ]]></help>
+    <expand macro="citations"/>
+</tool>