diff train.xml @ 0:08cc1cd58f38 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/train.xml	Fri Oct 14 21:42:14 2022 +0000
@@ -0,0 +1,154 @@
+<tool id="semibin_train" name="SemiBin: Train" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        the semi-supervised deep learning model
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#if $mode.select == 'single'
+    #if $mode.input_fasta.ext.endswith(".gz")
+gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
+    #else
+ln -s '$mode.input_fasta' 'contigs.fasta' &&
+    #end if
+#else
+    #for $e in $mode.input_fasta
+        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+        #if $e.ext.endswith(".gz")
+gunzip -c '$e' > '${identifier}.fasta' &&
+        #else
+ln -s '$e' '${identifier}.fasta' &&
+        #end if
+    #end for
+#end if
+SemiBin train
+    --mode '$mode.select'
+#if $mode.select == 'single'
+    --input-fasta 'contigs.fasta'
+    --data '$mode.data'
+    --data-split '$mode.data_split'
+    --cannot-link '$mode.cannot_link'
+#else
+    #for $e in $mode.input_fasta
+    --input-fasta '${e.element_identifier}.fasta'
+    #end for
+    #for $e in $mode.data
+    --data '$e'
+    #end for
+    #for $e in $mode.data_split
+    --data-split '$e'
+    #end for
+    #for $e in $mode.cannot_link
+    --cannot-link '$e'
+    #end for
+#end if
+    --output 'output'
+    --threads \${GALAXY_SLOTS:-1}
+    --epoches $epoches
+    --batch-size $batch_size
+    --random-seed $random_seed
+#if $min_len.method == 'min-len'
+    --min-len $min_len.min_len
+#else if $min_len.method == 'ratio'
+    --ratio $min_len.ratio
+#end if
+    --orf-finder '$orf_finder'
+    ]]></command>
+    <inputs>
+        <conditional name="mode">
+            <param argument="select" type="select" label="Mode to train the models">
+                <option value="single" selected="true">From one sample</option>
+                <option value="several">From multiple samples (train model across several samples can get better pre-trained model for single-sample binning)</option>
+            </param>
+            <when value="single">
+                <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
+                <param argument="--data" type="data"  format="csv" label="Train data"/>
+                <param argument="--data-split" type="data" format="csv" label="Split train data"/>
+                <param argument="--cannot-link" type="data" format="txt" label="Cannot-link constraints"/>
+            </when>
+            <when value="several">
+                <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
+                <param argument="--data" type="data" format="csv" multiple="true" label="Train data"/>
+                <param argument="--data-split" type="data" format="csv" multiple="true" label="Split train data"/>
+                <param argument="--cannot-link" type="data" format="txt" multiple="true" label="Cannot-link constraints"/>
+            </when>
+        </conditional>
+        <expand macro="min_len"/>
+        <expand macro="orf-finder"/>
+        <expand macro="random-seed"/>
+        <expand macro="epoches"/>
+        <expand macro="batch-size"/>
+    </inputs>
+    <outputs>
+        <expand macro="train_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <param name="data" ftype="csv" value="data.csv"/>
+                <param name="data_split" ftype="csv" value="data_split.csv"/>
+                <param name="cannot_link" ftype="txt" value="cannot.txt"/>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="2500" />
+            </conditional>
+            <param name="orf_finder" value="prodigal"/>
+            <param name="random-seed" value="0"/>
+            <param name="epoches" value="1"/>
+            <param name="batch_size" value="2048"/>
+            <output name="model" ftype="h5">
+                <assert_contents>
+                    <has_size value="3119000" delta="1000" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="several"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/>
+                <param name="data" ftype="csv" value="data.csv,data.csv,data.csv"/>
+                <param name="data_split" ftype="csv" value="data_split.csv,data_split.csv,data_split.csv"/>
+                <param name="cannot_link" ftype="txt" value="cannot.txt,cannot.txt,cannot.txt"/>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="ratio"/>
+                <param name="ratio" value="0.05" />
+            </conditional>
+            <param name="orf_finder" value="prodigal"/>
+            <param name="random-seed" value="0"/>
+            <param name="epoches" value="20"/>
+            <param name="batch_size" value="2048"/>
+            <output name="model" ftype="h5">
+                <assert_contents>
+                    <has_size value="3119000" delta="1000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool trains the semi-supervised deep learning model
+
+Inputs
+======
+
+@HELP_INPUT_FASTA@
+@HELP_CANNOT@
+@HELP_DATA@
+
+Outputs
+=======
+
+@HELP_MODEL@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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