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comparison axttomaf.xml @ 2:021202bf325f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
author iuc
date Thu, 26 Sep 2024 16:52:23 +0000
parents a030255ee7eb
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1:a030255ee7eb 2:021202bf325f
1 <tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> 1 <tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy1" profile="21.05" license="MIT">
2 <description> 2 <description>
3 Convert dataset from axt to MAF format 3 Convert dataset from axt to MAF format
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">469</token> 6 <token name="@TOOL_VERSION@">469</token>
7 <xml name="sanitize_query">
8 <sanitizer>
9 <valid initial="string.printable">
10 <remove value=" "/>
11 <remove value="&apos;" />
12 </valid>
13 <mapping initial="none">
14 <add source=" " target=""/>
15 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
16 </mapping>
17 </sanitizer>
18 </xml>
7 </macros> 19 </macros>
8 <xrefs> 20 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> 21 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs> 22 </xrefs>
11 <requirements> 23 <requirements>
23 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history": 35 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
24 '${query_reference_index_source.in_que_ref_index}' 36 '${query_reference_index_source.in_que_ref_index}'
25 #else: 37 #else:
26 '$query_reference_index_source.que_ref_index_file.fields.path' 38 '$query_reference_index_source.que_ref_index_file.fields.path'
27 #end if 39 #end if
40 #if str($t_prefix)
41 -tPrefix='$t_prefix'
42 #end if
43 #if str($q_prefix)
44 -qPrefix='$q_prefix'
45 #end if
46 $score
47 $scoreZero
28 '$out' 48 '$out'
29 ]]></command> 49 ]]></command>
30 <inputs> 50 <inputs>
31 <param name="in_axt" format="axt" type="data" label="axt file" /> 51 <param name="in_axt" format="axt" type="data" label="axt file" />
32 52
58 <when value="history"> 78 <when value="history">
59 <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." /> 79 <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
60 </when> 80 </when>
61 </conditional> 81 </conditional>
62 82
83 <param name="t_prefix" type="text" optional="true" label="add this to start of TARGET sequence name in maf" help="Typically organism name and a dot (hg38.) is used">
84 <expand macro="sanitize_query"/>
85 </param>
86 <param name="q_prefix" type="text" optional="true" label="add this to start of QUERY sequence name in maf" help="Typically organism name and a dot (mm10.) is used">
87 <expand macro="sanitize_query"/>
88 </param>
89 <param argument="-score" type="boolean" truevalue="-score" falsevalue="" label="Recalculate score" />
90 <param argument="-scoreZero" type="boolean" truevalue="-scoreZero" falsevalue="" label="Recalculate score if zero" />
63 </inputs> 91 </inputs>
64 <outputs> 92 <outputs>
65 <data name="out" format="maf" /> 93 <data name="out" format="maf" />
66 </outputs> 94 </outputs>
67 <tests> 95 <tests>
73 </conditional> 101 </conditional>
74 <conditional name="query_reference_index_source"> 102 <conditional name="query_reference_index_source">
75 <param name="query_reference_index_source_selector" value="history" /> 103 <param name="query_reference_index_source_selector" value="history" />
76 <param name="in_que_ref_index" value="mm39.fasta.fai"/> 104 <param name="in_que_ref_index" value="mm39.fasta.fai"/>
77 </conditional> 105 </conditional>
106 <output name="out" file="1.maf"/>
107 </test>
108 <test>
109 <param name="in_axt" value="2.axt"/>
110 <conditional name="target_reference_index_source">
111 <param name="target_reference_index_source_selector" value="history" />
112 <param name="in_tar_ref_index" value="hg38.noprefix.fasta.fai"/>
113 </conditional>
114 <conditional name="query_reference_index_source">
115 <param name="query_reference_index_source_selector" value="history" />
116 <param name="in_que_ref_index" value="mm39.noprefix.fasta.fai"/>
117 </conditional>
118 <param name="t_prefix" value="hg38." />
119 <param name="q_prefix" value="mm39." />
78 <output name="out" file="1.maf"/> 120 <output name="out" file="1.maf"/>
79 </test> 121 </test>
80 <test> 122 <test>
81 <param name="in_axt" value="1.axt"/> 123 <param name="in_axt" value="1.axt"/>
82 <conditional name="target_reference_index_source"> 124 <conditional name="target_reference_index_source">