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comparison bacteria_tradis.xml @ 5:8e4a4f240961 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 5aac8c4c9990e8796c8a4c55d6c900c03e6db3c0
author iuc
date Wed, 13 Mar 2024 14:56:52 +0000
parents d1855ded740a
children
comparison
equal deleted inserted replaced
4:d1855ded740a 5:8e4a4f240961
1 <tool id="bacteria_tradis" name="Bio-TraDis reads to counts" version="@TOOL_VERSION@+galaxy@VERSION@"> 1 <tool id="bacteria_tradis" name="Bio-TraDis reads to counts" version="@TOOL_VERSION@+galaxy@VERSION@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive">
8 <![CDATA[ 9 <![CDATA[
9 cp '${input_ref}' reference.fa && 10 cp '${input_ref}' reference.fa &&
10 ls '${input_fastq}' > file.txt && 11 ls '${input_fastq}' > file.txt &&
23 #end if 24 #end if
24 25
25 #if str($tranposon_tag.use) == "yes": 26 #if str($tranposon_tag.use) == "yes":
26 -m '$tranposon_tag.nb_mismatches' 27 -m '$tranposon_tag.nb_mismatches'
27 -t '$tranposon_tag.sequence' 28 -t '$tranposon_tag.sequence'
29 -td '$tranposon_tag.tagdir'
28 #end if 30 #end if
29 2>&1 31 2>&1
30 ]]> 32 ]]>
31 </command> 33 </command>
32 34
41 43
42 </param> 44 </param>
43 <when value="modify"> 45 <when value="modify">
44 46
45 <conditional name="set_kmers_options"> 47 <conditional name="set_kmers_options">
46 <param name="set" type="boolean" label="Modify kmers parameters" truevalue='yes' falsevalue='no' /> 48 <param name="set" type="select" label="Modify kmers parameters">
49 <option value="yes">Yes</option>
50 <option value="no">No</option>
51 </param>
47 <when value="yes"> 52 <when value="yes">
48 <param name="kmer_length" type="integer" value="" min="9" max="20" label=" Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." /> 53 <param name="kmer_length" type="integer" value="" min="9" max="20" label="Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." />
49 <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." /> 54 <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." />
50 </when> 55 </when>
51 <when value="no"> 56 <when value="no"/>
52 </when>
53 </conditional> 57 </conditional>
54 58
55 <param name="min_percentage" type="float" value="0.96" min="0" max="1" label="Minimum percentage of identical bases between read and reference (--smalt_y)" help="May be lowered to improve sensitivity in the case of low quality or short reads." /> 59 <param name="min_percentage" type="float" value="0.96" min="0" max="1" label="Minimum percentage of identical bases between read and reference (--smalt_y)" help="May be lowered to improve sensitivity in the case of low quality or short reads." />
56 <param name="duplicate_reads" type="boolean" truevalue="-1" falsevalue="0" label="Randomly assign position to reads that align in multiple location (--smalt_r)" help="If not, reads mapping in multiples positions are ignored" /> 60 <param name="duplicate_reads" type="boolean" truevalue="-1" falsevalue="0" label="Randomly assign position to reads that align in multiple location (--smalt_r)" help="If not, reads mapping in multiples positions are ignored" />
57 <param name="min_quality" type="integer" value="30" label="Minimum mapping quality score (-m) " help="Multi-mapping reads have a quality score of 0 by definition, so this parameter needs to be set to 0 for these reads to be properly processed. Can be lowered without dramatically affecting results in most cases, particularly if --smalt_y is set reasonably." /> 61 <param name="min_quality" type="integer" value="30" label="Minimum mapping quality score (-m) " help="Multi-mapping reads have a quality score of 0 by definition, so this parameter needs to be set to 0 for these reads to be properly processed. Can be lowered without dramatically affecting results in most cases, particularly if --smalt_y is set reasonably." />
60 <when value="default"> 64 <when value="default">
61 </when> 65 </when>
62 </conditional> 66 </conditional>
63 67
64 <conditional name="tranposon_tag"> 68 <conditional name="tranposon_tag">
65 <param name="use" type="boolean" truevalue="yes" falsevalue="no" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping." /> 69 <param name="use" type="select" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping.">
66 70 <option value="yes">Yes</option>
71 <option value="no">No</option>
72 </param>
67 <when value="yes"> 73 <when value="yes">
68
69 <param name="sequence" type="text" value="" help="" /> 74 <param name="sequence" type="text" value="" help="" />
70 <param name="nb_mismatches" type="integer" value="2" min="0" help="If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags." /> 75 <param name="nb_mismatches" type="integer" value="2" min="0" help="If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags." />
71 <param name="tagdir" type="select" label="Direction of the transposon tag" help="" > 76 <param name="tagdir" type="select" label="Direction of the transposon tag" help="" >
72 <option value="3" selected="true">3'</option> 77 <option value="3" selected="true">3'</option>
73 <option value="5">5bacteria_tradis.xml'</option> 78 <option value="5">5'</option>
74 </param> 79 </param>
75
76 </when> 80 </when>
77 <when value="no"> 81 <when value="no"/>
78 </when>
79 </conditional> 82 </conditional>
80 83
81 84
82 </inputs> 85 </inputs>
83 86