diff histex.xml @ 0:b897c5daf0ce draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 772b3643ac0ec68d8b322bb0e2b672d26c440a3a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/histex.xml	Wed Jan 08 11:03:09 2025 +0000
@@ -0,0 +1,72 @@
+<tool id="fastk_histex" name="FastK Histex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
+    <description>Reads and displays a kmer histogram produced by FastK</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_hist' input.hist &&
+        Histex input.hist
+        #if str($range_count_start).strip():
+            -h$range_count_start:$range_count_end
+        #end if
+        $select_output_format > output.hist
+    ]]></command>
+    <inputs>      
+        <param name="input_hist" type="data" format="fastk_hist" label="Input .hist file" help="Input a .hist file obtained from FASTK"/>
+        <param name="range_count_start" type="integer" min="1" label="Output histogram of counts in range given (Start)" optional="true" help="Enter the starting range for histogram of counts"/>
+        <param name="range_count_end" type="integer" max="100" label="Output histogram of counts in range given (End)" optional="true" help="Enter the ending range for histogram of counts"/>
+        <param name="select_output_format" label="Select the output format for Histogram" type="select">
+            <option value="-k">Output histogram of k-mer instance counts vs. unique k-mers (-k)</option>
+            <option value="-A">Output in simple tab-delimited ASCII format (-A)</option>
+            <option value="-G">Output an ASCII format histogram especially for GeneScope.FK (-G)</option>   
+        </param>
+    </inputs>
+    <outputs>
+        <data name="histex_out" format="txt" from_work_dir="output.hist" label="${tool.name} on ${on_string}: FastK Histogram Text">
+            <filter>select_output_format != '-A' </filter>
+        </data>
+        <data name="histex_out_tsv" format="tabular" from_work_dir="output.hist" label="${tool.name} on ${on_string}: FastK Histogram TSV">
+            <filter> select_output_format == '-A'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hist" value="test01.hist"/>
+            <param name="select_output_format" value="-k"/>
+            <output name="histex_out" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="13"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hist" value="test01.hist"/>
+            <param name="range_count_start" value="1"/>
+            <param name="range_count_end" value="5"/>
+            <param name="select_output_format" value="-k"/>
+            <output name="histex_out" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="11"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hist" value="test01.hist"/>
+            <param name="select_output_format" value="-A"/>
+            <output name="histex_out" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="7"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **FastK Histex**
+
+        Histex is a tool, part of FASTK suite that performs reading and displaying a kmer histogram produced by FastK. Histex requires the .hist file generated by the FASTK tool to view the histogram of k‑mer counts.
+    
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file