Mercurial > repos > iuc > stacks2_sstacks

comparison macros_process.xml @ 5:78bc438ccbfe 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 09:06:42 +0000
parents 51a693977534
children
comparison
equal deleted inserted replaced
4:b88af2e15eb4 5:78bc438ccbfe
2 2
3 <!-- macros and tokens for process_radtags and process_short_reads --> 3 <!-- macros and tokens for process_radtags and process_short_reads -->
4 4
5 <macros> 5 <macros>
6 6
7
7 <token name="@PROCESS_IOOPTIONS@"><![CDATA[ 8 <token name="@PROCESS_IOOPTIONS@"><![CDATA[
8 -p stacks_inputs/ 9 -p stacks_inputs/
9 #if $input_type.input_type_select == "paired" 10 #if $input_type.input_type_select == "paired"
10 --paired 11 --paired
11 #end if 12 #end if
12 -i $inputype 13 -i $inputype
13 -b '$barcode'
14 $input_type.barcode_encoding 14 $input_type.barcode_encoding
15 #if $input_type.barcode_encoding != ''
16 -b '$input_type.barcode'
17 #end if
15 #if str( $outype ) != "auto" 18 #if str( $outype ) != "auto"
16 -y $outype 19 -y $outype
17 #end if 20 #end if
18 -o stacks_outputs 21 -o stacks_outputs
19 ]]></token> 22 ]]></token>
36 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/> 39 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/>
37 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/> 40 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/>
38 </xml> 41 </xml>
39 42
40 <xml name="process_outputs"> 43 <xml name="process_outputs">
41 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads"> 44 <yield/>
42 <filter>input_type['input_type_select'] == "single"</filter>
43 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
44 </collection>
45 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
46 <filter>input_type['input_type_select'] == "paired"</filter>
47 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
48 </collection>
49
50 <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads"> 45 <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
51 <filter>input_type['input_type_select'] == "paired"</filter> 46 <filter>input_type['input_type_select'] == "paired"</filter>
52 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/> 47 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
53 </collection> 48 </collection>
54
55 <!-- note irrespective of -y output is always named fastq and are never zipped --> 49 <!-- note irrespective of -y output is always named fastq and are never zipped -->
56 <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads"> 50 <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
57 <filter>capture is True and input_type['input_type_select'] == "single"</filter> 51 <filter>capture is True and input_type['input_type_select'] == "single"</filter>
58 <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/> 52 <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
59 </collection> 53 </collection>
76 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/> 70 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/>
77 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> 71 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
78 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/> 72 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/>
79 </when> 73 </when>
80 <when value="no"> 74 <when value="no">
81 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> 75 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="Useful if your data has already been trimmed"/>
82 </when> 76 </when>
83 </conditional> 77 </conditional>
84 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/> 78 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
85 </xml> 79 </xml>
86 <token name="@PROCESS_FILTER@"><![CDATA[ 80 <token name="@PROCESS_FILTER@"><![CDATA[