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comparison histex.xml @ 0:323e5ebf6d5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 772b3643ac0ec68d8b322bb0e2b672d26c440a3a
author iuc
date Wed, 08 Jan 2025 11:02:29 +0000
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children c0bcbd03d352
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-1:000000000000 0:323e5ebf6d5d
1 <tool id="fastk_histex" name="FastK Histex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
2 <description>Reads and displays a kmer histogram produced by FastK</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_hist' input.hist &&
9 Histex input.hist
10 #if str($range_count_start).strip():
11 -h$range_count_start:$range_count_end
12 #end if
13 $select_output_format > output.hist
14 ]]></command>
15 <inputs>
16 <param name="input_hist" type="data" format="fastk_hist" label="Input .hist file" help="Input a .hist file obtained from FASTK"/>
17 <param name="range_count_start" type="integer" min="1" label="Output histogram of counts in range given (Start)" optional="true" help="Enter the starting range for histogram of counts"/>
18 <param name="range_count_end" type="integer" max="100" label="Output histogram of counts in range given (End)" optional="true" help="Enter the ending range for histogram of counts"/>
19 <param name="select_output_format" label="Select the output format for Histogram" type="select">
20 <option value="-k">Output histogram of k-mer instance counts vs. unique k-mers (-k)</option>
21 <option value="-A">Output in simple tab-delimited ASCII format (-A)</option>
22 <option value="-G">Output an ASCII format histogram especially for GeneScope.FK (-G)</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="histex_out" format="txt" from_work_dir="output.hist" label="${tool.name} on ${on_string}: FastK Histogram Text">
27 <filter>select_output_format != '-A' </filter>
28 </data>
29 <data name="histex_out_tsv" format="tabular" from_work_dir="output.hist" label="${tool.name} on ${on_string}: FastK Histogram TSV">
30 <filter> select_output_format == '-A'</filter>
31 </data>
32 </outputs>
33 <tests>
34 <test expect_num_outputs="1">
35 <param name="input_hist" value="test01.hist"/>
36 <param name="select_output_format" value="-k"/>
37 <output name="histex_out" ftype="txt">
38 <assert_contents>
39 <has_n_lines n="13"/>
40 </assert_contents>
41 </output>
42 </test>
43 <test expect_num_outputs="1">
44 <param name="input_hist" value="test01.hist"/>
45 <param name="range_count_start" value="1"/>
46 <param name="range_count_end" value="5"/>
47 <param name="select_output_format" value="-k"/>
48 <output name="histex_out" ftype="txt">
49 <assert_contents>
50 <has_n_lines n="11"/>
51 </assert_contents>
52 </output>
53 </test>
54 <test expect_num_outputs="1">
55 <param name="input_hist" value="test01.hist"/>
56 <param name="select_output_format" value="-A"/>
57 <output name="histex_out" ftype="tabular">
58 <assert_contents>
59 <has_n_lines n="7"/>
60 <has_n_columns n="2"/>
61 </assert_contents>
62 </output>
63 </test>
64 </tests>
65 <help><![CDATA[
66 **FastK Histex**
67
68 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.
69
70 ]]></help>
71 <expand macro="citations"/>
72 </tool>