diff fasta_clipping_histogram.xml @ 4:40ec4170291e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1

--- a/fasta_clipping_histogram.xml	Tue Oct 13 12:38:50 2015 -0400
+++ b/fasta_clipping_histogram.xml	Tue May 08 10:45:30 2018 -0400
@@ -1,20 +1,35 @@
-<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
     <description>chart</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>fasta_clipping_histogram.pl $input $outfile</command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.49">perl-gdgraph</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+fasta_clipping_histogram.pl
+'$input'
+'$outfile'
+    ]]></command>
 
     <inputs>
-        <param format="fasta" name="input" type="data" label="Library to analyze" />
+        <expand macro="fasta_input" />
     </inputs>
 
     <outputs>
-        <data format="png" name="outfile" metadata_source="input" />
+        <data name="outfile" format="png" metadata_source="input" />
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in1.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out1.png" compare="sim_size" delta="512" />
+        </test>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in2.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out2.png" compare="sim_size" delta="512" />
+        </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
@@ -41,19 +56,19 @@
 
 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
 
-   >sequence1
-   AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
-   >sequence2
-   GTGTGTGTGGGAAGTTGACACAGTA
-   >sequence3
-   CCTTGAGATTAACGCTAATCAAGTAAAC
+    >sequence1
+    AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+    >sequence2
+    GTGTGTGTGGGAAGTTGACACAGTA
+    >sequence3
+    CCTTGAGATTAACGCTAATCAAGTAAAC
 
 If the sequences span over multiple lines::
 
-   >sequence1
-   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
-   TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
-   aactggtctttacctTTAAGTTG
+    >sequence1
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
 
 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
 
@@ -98,6 +113,7 @@
 
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
- .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+.. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
 </tool>