Mercurial > repos > iuc > flair_correct

annotate flair_correct.xml @ 0:6927379c9ede draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
author iuc
date Fri, 27 Nov 2020 21:55:45 +0000
parents
children c784170f3b5e
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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1 <tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@" profile="20.01">
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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2 <description>corrects misaligned splice sites using genome annotations</description>
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3
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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4 <macros>
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5 <import>flair_macros.xml</import>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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6 </macros>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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7
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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11 <command detect_errors="exit_code"><![CDATA[
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12
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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13 @PREPARE_REF@
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14
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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15 flair.py correct
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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17 ###########
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18 ## Input ##
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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19 ###########
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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21 -q '$input_query'
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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22 -g reference.fa
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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23 -f '$input_gtf'
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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25 #if $input_shortread:
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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26 -j '$input_shortread'
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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27 #end if
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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29 ########################
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30 ## Additional Options ##
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31 ########################
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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32
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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33 $additional_options.strand
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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34 -w $additional_options.window
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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35
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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36 #########
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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37 ## END ##
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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38 #########
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39
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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40 ]]></command>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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41 <inputs>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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42 <param name="input_query" argument="-q" type="data" format="bed12" label="Uncorrected Bed12 file"/>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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43 <expand macro="reference_interface" />
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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44 <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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45 <param name="input_shortread" optional="true" argument="-j" type="data" format="bed" label="Splice junction BED file" />
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46
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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47 <!-- Additional Options -->
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48 <section name="additional_options" title="Additional Options">
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49 <param name="strand" argument="-n" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Strand Consistency" help="Keep the strand of a read consistent after correction."/>
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50 <param name="window" argument="-w" type="integer" min="1" value="10" label="Window Size" help="Window size for correcting splice sites (Default=10)" />
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51 </section>
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52 </inputs>
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53
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54
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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55 <outputs>
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56 <data name="outfile_1" format="bed12" from_work_dir="flair_all_corrected.bed" label="${tool.name} on ${on_string}: Corrected Reads" />
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57 <data name="outfile_2" format="bed12" from_work_dir="flair_all_inconsistent.bed" label="${tool.name} on ${on_string}: Inconsistent Reads" />
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58 </outputs>
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59
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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60 <tests>
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61 <test expect_num_outputs="2">
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62 <param name="input_query" ftype="bed12" value="chrM.bed12" />
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63 <param name="ref_selector_genome" value="history" />
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64 <param name="reffile" ftype="fasta" value="chrM.fa" />
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65 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
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66 <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" />
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67 <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" />
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68 </test>
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69 <!-- Test with cached genome -->
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70 <test expect_num_outputs="2">
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71 <param name="input_query" ftype="bed12" value="chrM.bed12" />
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72 <param name="ref_selector_genome" value="cached" />
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73 <param name="reffile" value="chrM" />
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74 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
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75 <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" />
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76 <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" />
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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82 .. class:: infomark
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83
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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84 **What it does**
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85
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86 -------------------
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87
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88 @description@
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89
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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90 **flair correct**
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91 Corrects misaligned splice sites using genome annotations and/or short-read splice junctions. Based on common user issues we have encountered, for flair-correct to run properly, please ensure/note that (1) the genome annotation and genome sequences are compatible, (2) gtf is preferred over gff for annotation and annotations that do not split single exons into multiple entries are ideal.
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92
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93 -------------------
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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94
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95 **Inputs**
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96
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97 -------------------
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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98
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99 (1) Uncorreced bed12 file.
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100 (2) FASTA file of the reference genome.
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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101 (3) GTF annotation file.
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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102 (4) BED format splice junctions from short-read sequencing or GTF annotation file.
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103
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104 -----------
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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105
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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106 **Outputs**
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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107
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108 -----------
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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109
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110 (1) bed12 of corrected reads,
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111 (2) bed12 of reads that weren't able to be corrected,
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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112 (3) psl of corrected reads if the -c chromsizes file is provided.
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113
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114 Either (1) or (3) can be supplied to flair-collapse as the query.
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115
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116 --------------------
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117
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118 **More Information**
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119
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120 --------------------
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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121
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122 See the excellent `FLAIR documentation`_
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123
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124 .. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair
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125
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126
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127 --------------------
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128
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129 **Galaxy Wrapper Development**
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130
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131 --------------------
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132
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133 @citation@
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134
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135 ]]></help>
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136 <expand macro="citations" />
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137 </tool>