diff assembly-stats.xml @ 0:9e4955725212 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats commit 28119c39c4b59a67f629c8ca569d58f4d2949c9c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assembly-stats.xml	Wed Jun 21 09:26:46 2023 +0000
@@ -0,0 +1,75 @@
+<?xml version="1.0"?>
+<tool id="assembly_stats" name="Assembly stats" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>visualisations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rjchallis-assembly-stats</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $output_format == "html"
+            SRC="\$(dirname \$(which asm2stats.pl))/../opt/assembly-stats" &&
+            mkdir -p $output.files_path &&
+            
+            cp -r "\$SRC/css/" '$output.files_path'  &&
+            cp -r "\$SRC/js/" '$output.files_path'  &&
+            cp '$__tool_directory__/d3-tip.js' '${output.files_path}/js/d3-tip.js' && 
+            mkdir -p '$output.files_path/json/' &&
+            cp '$__tool_directory__/assembly-stats.html' '$output' && 
+            cp '$__tool_directory__/assembly-stats.html' '${output.files_path}' && 
+
+            asm2stats.minmaxgc.pl '${input_fasta}' > '${output.files_path}/json/output.assembly-stats.json' ######
+        #else
+            asm2stats.minmaxgc.pl '${input_fasta}' > '${output}'
+        #end if
+
+    ]]></command>
+
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" label="Genome assembly"/>
+        <param name="output_format" type="select" label="Output format" >
+            <option value="html" selected="true">HTML</option>
+            <option value="json">JSON</option>
+        </param>
+    </inputs>
+    
+    <outputs>
+        <data name="output" format="html" label="Assembly-stats on ${on_string}" >
+            <change_format>
+                <when input="output_format" value="json" format="json" />
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="sequence.fasta"/>
+            <param name="output_format" value="json"/>
+            <output name="output" ftype="json">
+                <assert_contents>
+                    <has_text text='"contig_count" : 1' />
+                    <has_text text='"scaffold_count" : 1' />
+                    <has_text text='154478' />
+                    <has_text text='"GC" : 36.29' />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="sequence.fasta"/>
+            <param name="output_format" value="html"/>
+            <output name="output" value="assembly-stats.html" ftype="html">
+                <assert_contents>
+                    <has_size value="7819"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+        assembly_stats_ Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.
+
+        .. _assembly_stats: https://github.com/rjchallis/assembly-stats
+    ]]></help>
+    <expand macro="citation"/>
+</tool>