Mercurial > repos > iuc > colibread_kissplice

annotate kissplice.xml @ 6:7c02beb8ba3d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:54:14 +0000
parents 7d4435f9c77d
children
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6
7c02beb8ba3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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1 <tool id="kissplice" name="KisSplice" version="2.4.0+galaxy1" profile="@PROFILE@">
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2 <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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3 <macros>
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4 <import>macros.xml</import>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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5 </macros>
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6 <requirements>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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7 <requirement type="package" version="2.4.0p1">kissplice</requirement>
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8 </requirements>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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9 <version_command>kissplice --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set $samples = ""
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12 #for input in $list_reads
7d4435f9c77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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13 @single_reads@
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14 #set $samples += " -r '" + $filename + "'"
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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15 #end for
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16 kissplice
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17 $samples
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18 -k ${k}
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19 -c ${c}
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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20 -C ${C}
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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21 ${output_context}
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22 --counts ${counts}
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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23 ]]></command>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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24 <inputs>
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25 <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" />
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4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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26 <param argument="-k" type="integer" value="41" label="K-mer length" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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27 <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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28 <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
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29 <param argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
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30 <param argument="--counts" type="select" label="Selecting how the counts will be reported">
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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31 <option value="0">Total counts</option>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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32 <option value="1">Counts on junctions</option>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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33 <option value="2">All counts</option>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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34 </param>
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35 <param name="output_option" type="select" label="Output type">
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36 <option value="alternative_file">Generate only the Alternative Splicing file</option>
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37 <option value="all_files">Generate all files</option>
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38 </param>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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39 </inputs>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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40 <outputs>
6
7c02beb8ba3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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41 <data name="type0a" format="fasta" label="${tool.name} on ${on_string}: Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
0
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42 <filter>output_option == 'all_files'</filter>
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43 </data>
6
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44 <data name="type0b" format="fasta" label="${tool.name} on ${on_string}: Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
0
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45 <filter>output_option == 'all_files'</filter>
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46 </data>
6
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47 <data name="type1" format="fasta" label="${tool.name} on ${on_string}: Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
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48 <data name="type2" format="fasta" label="${tool.name} on ${on_string}: Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
0
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49 <filter>output_option == 'all_files'</filter>
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50 </data>
6
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51 <data name="type3" format="fasta" label="${tool.name} on ${on_string}: Short indels" from_work_dir="results/*_coherents_type_3.fa">
0
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52 <filter>output_option == 'all_files'</filter>
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53 </data>
6
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54 <data name="type4" format="fasta" label="${tool.name} on ${on_string}: Other events" from_work_dir="results/*_coherents_type_4.fa">
0
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55 <filter>output_option == 'all_files'</filter>
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56 </data>
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57 </outputs>
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58 <tests>
6
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59 <test expect_num_outputs="1">
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60 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
0
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61 <param name="k" value="25"/>
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62 <param name="output_option" value="alternative_file" />
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63 <output name="type1" file="kissplice/alternative_splicing.fa"/>
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64 </test>
6
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65 <test expect_num_outputs="6">
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66 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
7c02beb8ba3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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67 <param name="k" value="25"/>
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68 <param name="output_option" value="all_files" />
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69 <output name="type0a">
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70 <assert_contents>
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71 <has_n_lines n="0"/>
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72 </assert_contents>
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73 </output>
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74 <output name="type0b">
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75 <assert_contents>
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76 <has_n_lines n="0"/>
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77 </assert_contents>
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78 </output>
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79 <output name="type1" file="kissplice/alternative_splicing.fa"/>
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80 <output name="type2">
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81 <assert_contents>
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82 <has_n_lines n="0"/>
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83 </assert_contents>
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84 </output>
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85 <output name="type3">
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86 <assert_contents>
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87 <has_n_lines n="0"/>
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88 </assert_contents>
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89 </output>
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90 <output name="type4">
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91 <assert_contents>
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92 <has_n_lines n="0"/>
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93 </assert_contents>
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94 </output>
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95 </test>
0
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96 </tests>
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97 <help><![CDATA[
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98
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99 **Description**
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100
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101 KisSplice is a piece of software that enables the **analysis of RNA-seq data with or without a reference genome**. It is an exact local transcriptome assembler that allows one to identify **SNPs, indels and alternative splicing events**. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.
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102
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103 KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely. However, KisSplice results can be further aligned to a reference transcriptome (if available), or to the output of a full-length transcriptome assembler like Trinity or Oases.
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104
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105 ------
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106
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107 **Website**
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108
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109 References, documentation and FAQ here_.
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110
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111 .. _here: http://kissplice.prabi.fr/
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112
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113
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114 ]]></help>
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115 <expand macro="citations">
6
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116 <citation type="doi">10.1186/1471-2105-13-S6-S5</citation>
0
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117 </expand>
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118
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119 </tool>