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comparison rseqc_macros.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
comparison
equal deleted inserted replaced
59:dbedfc5f5a3c 60:1421603cc95b
1 <macros> 1 <macros>
2 2 <token name="@TOOL_VERSION@">5.0.1</token>
3 <token name="@TOOL_VERSION@">2.6.4</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 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="2.6.4">rseqc</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 <xml name="bio_tools"> 11 <xml name="bio_tools">
12 <xrefs> 12 <xrefs>
20 </stdio> 20 </stdio>
21 </xml> 21 </xml>
22 22
23 <!-- Params --> 23 <!-- Params -->
24 <xml name="bam_param"> 24 <xml name="bam_param">
25 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> 25 <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
26 </xml> 26 </xml>
27 27
28 <xml name="bam_sam_param"> 28 <xml name="bam_sam_param">
29 <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/> 29 <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
30 </xml> 30 </xml>
31 31
32 <xml name="refgene_param"> 32 <xml name="refgene_param">
33 <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/> 33 <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
34 </xml> 34 </xml>
35 35
36 <xml name="mapq_param"> 36 <xml name="mapq_param">
37 <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/> 37 <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30"
38 help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
38 </xml> 39 </xml>
39 40
40 <xml name="readlength_param"> 41 <xml name="readlength_param">
41 <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/> 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"/>
42 </xml> 43 </xml>
43 44
44 <xml name="readnum_param"> 45 <xml name="readnum_param">
45 <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/> 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"/>
46 </xml> 47 </xml>
47 48
48 <xml name="sample_size_param"> 49 <xml name="sample_size_param">
49 <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/> 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"/>
50 </xml> 51 </xml>
51 52
52 <xml name="min_intron_param"> 53 <xml name="min_intron_param">
53 <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" /> 54 <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
54 </xml> 55 </xml>
55 56
56 <xml name="layout_param"> 57 <xml name="layout_param">
57 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)"> 58 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
58 <option value="SE" selected="true">Single-end</option> 59 <option value="SE" selected="true">Single-end</option>
117 <filter>rscript_output</filter> 118 <filter>rscript_output</filter>
118 </data> 119 </data>
119 </xml> 120 </xml>
120 121
121 <!-- Command --> 122 <!-- Command -->
122 <token name="@MULTIHITS@"> 123 <token name="@MULTIHITS@"><![CDATA[
123 <![CDATA[ 124 #if str($multihits_type.multihits_type_selector) == "skip_multihits"
124 #if str($multihits_type.multihits_type_selector) == "skip_multihits" 125 --skip-multi-hits
125 --skip-multi-hits 126 --mapq=${multihits_type.mapq}
126 --mapq=${multihits_type.mapq} 127 #end if
127 #end if 128 ]]></token>
128 ]]> 129
129 </token> 130 <token name="@BAM_SAM_INPUTS@"><![CDATA[
131 #set $extension = str($input.ext)
132 ln -s -f '${input}' 'input.${extension}' &&
133 #if $extension == 'bam'
134 ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
135 #end if
136 ]]></token>
130 137
131 <token name="@ABOUT@"> 138 <token name="@ABOUT@">
132 139
133 ----- 140 -----
134 141