Mercurial > repos > iuc > semibin_concatenate_fasta

diff concatenate_fasta.xml @ 0:dcc81bfe5f6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
author iuc
date Fri, 14 Oct 2022 21:51:40 +0000
parents
children e6bc3455940e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concatenate_fasta.xml	Fri Oct 14 21:51:40 2022 +0000
@@ -0,0 +1,65 @@
+<tool id="semibin_concatenate_fasta" name="SemiBin: Concatenate fasta files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        for multi-sample binning
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#for $e in $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' '${identifier}.fasta' &&
+    #end if
+#end for
+
+SemiBin concatenate_fasta
+    --input-fasta *.fasta
+    --output 'output'
+    --separator '$separator'
+    -m $min_len
+    ]]></command>
+    <inputs>
+        <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
+        <expand macro="separator"/>
+        <expand macro="concat_min_len"/>
+    </inputs>
+    <outputs>
+        <data name="fasta" format="fasta" from_work_dir="output/concatenated.fa" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/>
+            <param name="separator" value=":"/>
+            <param name="min_len" value="0"/>
+            <output name="fasta" ftype="fasta">
+                <assert_contents>
+                    <has_text text=">input_single:g1k_0"/>
+                    <has_text text=">input_single_3:g4k_7"/>
+                    <has_text text=">input_single_2:g1k_0"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Inputs
+======
+
+@HELP_INPUT_FASTA@
+
+Outputs
+=======
+
+- One fasta with all contigs
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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