Mercurial > repos > iuc > flair_correct

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
author iuc
date Fri, 09 Apr 2021 21:15:31 +0000
parents 6927379c9ede
children
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c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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1 <tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@+galaxy0" profile="20.01">
0
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2 <description>corrects misaligned splice sites using genome annotations</description>
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3
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4 <macros>
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5 <import>flair_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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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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13 @PREPARE_REF@
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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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15 flair.py correct
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17 ###########
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18 ## Input ##
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19 ###########
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21 -q '$input_query'
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22 -g reference.fa
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23 -f '$input_gtf'
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25 #if $input_shortread:
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26 -j '$input_shortread'
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27 #end if
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29 ########################
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30 ## Additional Options ##
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31 ########################
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33 $additional_options.strand
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34 -w $additional_options.window
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36 #########
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37 ## END ##
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38 #########
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39
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40 ]]></command>
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41 <inputs>
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42 <param name="input_query" argument="-q" type="data" format="bed12" label="Uncorrected Bed12 file"/>
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43 <expand macro="reference_interface" />
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44 <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
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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
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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
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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
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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
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82 .. class:: infomark
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83
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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
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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>