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comparison stacks_shortreads.xml @ 5:4e280b27a831 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:25:46 +0000
parents c5d7050e4ad7
children
comparison
equal deleted inserted replaced
4:17d39bf0a63a 5:4e280b27a831
1 <!-- this is essentially a copy of stacks_procrad minus the unsupported options --> 1 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
2 <tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 2 <tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description> 3 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_process.xml</import> 6 <import>macros_process.xml</import>
7 </macros> 7 </macros>
18 $link_command 18 $link_command
19 19
20 20
21 process_shortreads 21 process_shortreads
22 22
23 @PROCESS_IOOPTIONS@ 23 -p stacks_inputs/
24 #if $input_type.input_type_select == "paired"
25 --paired
26 #end if
27 -i $inputype
28 -b '$barcode'
29 $input_type.barcode_encoding
30 #if str( $outype ) != "auto"
31 -y $outype
32 #end if
33 -o stacks_outputs
24 @PROCESS_FILTER@ 34 @PROCESS_FILTER@
25 @COMMON_ADVANCED@ 35 @COMMON_ADVANCED@
26 @RESCUE_BARCODE@ 36 @RESCUE_BARCODE@
27 @PROCESS_ADAPTER@ 37 @PROCESS_ADAPTER@
28 38
44 <expand macro="rescue_barcode"/> 54 <expand macro="rescue_barcode"/>
45 <expand macro="process_adapter"/> 55 <expand macro="process_adapter"/>
46 </section> 56 </section>
47 <expand macro="process_filter"/> 57 <expand macro="process_filter"/>
48 <expand macro="process_output_types"/> 58 <expand macro="process_output_types"/>
59 <expand macro="in_log"/>
49 </inputs> 60 </inputs>
50 61
51 <outputs> 62 <outputs>
52 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log"> 63 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log">
53 <filter>add_log</filter> 64 <filter>add_log</filter>
54 </data> 65 </data>
55 <expand macro="process_outputs"/> 66 <expand macro="process_outputs">
67 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
68 <filter>input_type['input_type_select'] == "single"</filter>
69 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
70 </collection>
71 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
72 <filter>input_type['input_type_select'] == "paired"</filter>
73 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
74 </collection>
75 </expand>
56 </outputs> 76 </outputs>
57 77
58 <tests> 78 <tests>
59 <!-- test single end, default options --> 79 <!-- test single end, default options -->
60 <test expect_num_outputs="2"> 80 <test expect_num_outputs="2">
61 <param name="input_type|input_type_select" value="single"/> 81 <param name="input_type|input_type_select" value="single"/>
62 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> 82 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/>
63 <param name="input_type|barcode_encoding" value="--inline_null"/> 83 <param name="input_type|barcode_encoding" value="--inline_null"/>
64 <param name="barcode" value="procrad/barcodes"/> 84 <param name="barcode" value="procrad/barcodes"/>
65 <param name="add_log" value="yes"/> 85 <param name="add_log" value="yes"/>
66 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/> 86 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
67 <output_collection name="demultiplexed" count="40"> 87 <output_collection name="demultiplexed" count="40">
68 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger"/> 88 <element name="PopA_01">
89 <assert_contents>
90 <has_size value="34964" delta="100"/>
91 <has_text text="@lane1_fakedata9_0 1:N:0:/1"/>
92 </assert_contents>
93 </element>
69 </output_collection> 94 </output_collection>
70 </test> 95 </test>
71 <!-- test single end, default options --> 96 <!-- test single end, default options -->
72 <test expect_num_outputs="4"> 97 <test expect_num_outputs="4">
73 <param name="input_type|input_type_select" value="paired"/> 98 <param name="input_type|input_type_select" value="paired"/>
74 <param name="input_type|fqinputs"> 99 <param name="input_type|fqinputs">
75 <collection type="list:paired"> 100 <collection type="list:paired">
76 <element name="reads"> 101 <element name="reads">
77 <collection type="paired"> 102 <collection type="paired">
78 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/> 103 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/>
79 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> 104 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
80 </collection> 105 </collection>
81 </element> 106 </element>
82 </collection> 107 </collection>
83 </param> 108 </param>
84 <param name="input_type|barcode_encoding" value="--inline_null"/> 109 <param name="input_type|barcode_encoding" value="--inline_null"/>