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comparison rseqc_macros.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">5.0.1</token> 2 <token name="@TOOL_VERSION@">5.0.3</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@GALAXY_VERSION@">20.01</token> 4 <token name="@GALAXY_VERSION@">20.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
8 <yield/> 8 <yield/>
13 <xref type="bio.tools">rseqc</xref> 13 <xref type="bio.tools">rseqc</xref>
14 </xrefs> 14 </xrefs>
15 </xml> 15 </xml>
16 <xml name="stdio"> 16 <xml name="stdio">
17 <stdio> 17 <stdio>
18 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 18 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information"/>
19 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 19 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information"/>
20 </stdio> 20 </stdio>
21 </xml> 21 </xml>
22
23 <!-- Params --> 22 <!-- Params -->
24 <xml name="bam_param"> 23 <xml name="bam_param">
25 <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/> 24 <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
26 </xml> 25 </xml>
27
28 <xml name="bam_sam_param"> 26 <xml name="bam_sam_param">
29 <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/> 27 <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
30 </xml> 28 </xml>
31
32 <xml name="refgene_param"> 29 <xml name="refgene_param">
33 <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/> 30 <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
34 </xml> 31 </xml>
35
36 <xml name="mapq_param"> 32 <xml name="mapq_param">
37 <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" 33 <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
38 help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
39 </xml> 34 </xml>
40
41 <xml name="readlength_param"> 35 <xml name="readlength_param">
42 <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/> 36 <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/>
43 </xml> 37 </xml>
44
45 <xml name="readnum_param"> 38 <xml name="readnum_param">
46 <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/> 39 <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/>
47 </xml> 40 </xml>
48
49 <xml name="sample_size_param"> 41 <xml name="sample_size_param">
50 <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/> 42 <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/>
51 </xml> 43 </xml>
52
53 <xml name="min_intron_param"> 44 <xml name="min_intron_param">
54 <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" /> 45 <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50"/>
55 </xml> 46 </xml>
56
57 <xml name="layout_param"> 47 <xml name="layout_param">
58 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)"> 48 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
59 <option value="SE" selected="true">Single-end</option> 49 <option value="SE" selected="true">Single-end</option>
60 <option value="PE">Paired-end</option> 50 <option value="PE">Paired-end</option>
61 </param> 51 </param>
62 </xml> 52 </xml>
63
64 <xml name="strand_type_param"> 53 <xml name="strand_type_param">
65 <conditional name="strand_type"> 54 <conditional name="strand_type">
66 <param name="strand_specific" type="select" label="Strand-specific?"> 55 <param name="strand_specific" type="select" label="Strand-specific?">
67 <option value="none" selected="true">None</option> 56 <option value="none" selected="true">None</option>
68 <option value="pair">Pair-End RNA-seq</option> 57 <option value="pair">Pair-End RNA-seq</option>
69 <option value="single">Single-End RNA-seq</option> 58 <option value="single">Single-End RNA-seq</option>
70 </param> 59 </param>
71 <when value="pair"> 60 <when value="pair">
72 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)"> 61 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --&gt; parent)" help="(--strand)">
73 <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> 62 <option value="sd" selected="true"> read1 (positive --&gt; positive; negative --&gt; negative), read2 (positive --&gt; negative; negative --&gt; positive)</option>
74 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> 63 <option value="ds">read1 (positive --&gt; negative; negative --&gt; positive), read2 (positive --&gt; positive; negative --&gt; negative)</option>
75 </param> 64 </param>
76 </when> 65 </when>
77 <when value="single"> 66 <when value="single">
78 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)"> 67 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --&gt; parent)" help="(--strand)">
79 <option value="s" selected="true">positive --> positive; negative --> negative</option> 68 <option value="s" selected="true">positive --&gt; positive; negative --&gt; negative</option>
80 <option value="d">positive --> negative; negative --> positive</option> 69 <option value="d">positive --&gt; negative; negative --&gt; positive</option>
81 </param> 70 </param>
82 </when> 71 </when>
83 <when value="none"></when> 72 <when value="none"/>
84 </conditional> 73 </conditional>
85 </xml> 74 </xml>
86
87 <xml name="multihits_param"> 75 <xml name="multihits_param">
88 <conditional name="multihits_type"> 76 <conditional name="multihits_type">
89 <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)"> 77 <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
90 <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option> 78 <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
91 <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option> 79 <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
92 </param> 80 </param>
93 <when value="skip_multihits"> 81 <when value="skip_multihits">
94 <expand macro="mapq_param" /> 82 <expand macro="mapq_param"/>
95 </when> 83 </when>
96 <when value="use_multihits" /> 84 <when value="use_multihits"/>
97 </conditional> 85 </conditional>
98 </xml> 86 </xml>
99
100 <xml name="rscript_output_param"> 87 <xml name="rscript_output_param">
101 <param name="rscript_output" type="boolean" value="false" label="Output R-Script" 88 <param name="rscript_output" type="boolean" value="false" label="Output R-Script" help="Output the R-Script used to generate the plots"/>
102 help="Output the R-Script used to generate the plots" />
103 </xml> 89 </xml>
104
105
106 <!-- Output --> 90 <!-- Output -->
107
108 <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF"> 91 <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF">
109 <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" /> 92 <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@"/>
110 </xml> 93 </xml>
111
112 <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS"> 94 <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS">
113 <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> 95 <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@"/>
114 </xml> 96 </xml>
115
116 <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript"> 97 <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript">
117 <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@"> 98 <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@">
118 <filter>rscript_output</filter> 99 <filter>rscript_output</filter>
119 </data> 100 </data>
120 </xml> 101 </xml>
121
122 <!-- Command --> 102 <!-- Command -->
123 <token name="@MULTIHITS@"><![CDATA[ 103 <token name="@MULTIHITS@"><![CDATA[
124 #if str($multihits_type.multihits_type_selector) == "skip_multihits" 104 #if str($multihits_type.multihits_type_selector) == "skip_multihits"
125 --skip-multi-hits 105 --skip-multi-hits
126 --mapq=${multihits_type.mapq} 106 --mapq=${multihits_type.mapq}
127 #end if 107 #end if
128 ]]></token> 108 ]]></token>
129
130 <token name="@BAM_SAM_INPUTS@"><![CDATA[ 109 <token name="@BAM_SAM_INPUTS@"><![CDATA[
131 #set $extension = str($input.ext) 110 #set $extension = str($input.ext)
132 ln -s -f '${input}' 'input.${extension}' && 111 ln -s -f '${input}' 'input.${extension}' &&
133 #if $extension == 'bam' 112 #if $extension == 'bam'
134 ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' && 113 ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
135 #end if 114 #end if
136 ]]></token> 115 ]]></token>
137
138 <token name="@ABOUT@"> 116 <token name="@ABOUT@">
139 117
140 ----- 118 -----
141 119
142 About RSeQC 120 About RSeQC
156 134
157 .. _RSeQC: http://rseqc.sourceforge.net/ 135 .. _RSeQC: http://rseqc.sourceforge.net/
158 136
159 137
160 </token> 138 </token>
161
162 <xml name="citations"> 139 <xml name="citations">
163 <citations> 140 <citations>
164 <citation type="doi">10.1093/bioinformatics/bts356</citation> 141 <citation type="doi">10.1093/bioinformatics/bts356</citation>
165 </citations> 142 </citations>
166 </xml> 143 </xml>