Mercurial > repos > iuc > chira_extract

annotate chira_extract.xml @ 11:a618f28e1496 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
author iuc
date Sun, 14 Jun 2020 17:37:05 -0400
parents 7ec1d063fecd
children 97ca48f470ef
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0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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1 <tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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2 <description>extrat the chimeras</description>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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8 #set $genomic_fasta = ''
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9 #if str($annotation.annot_choice) == "yes":
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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10 #if str($annotation.fasta_source.fasta_source_selector) == 'history':
2
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11 #set $genomic_fasta = $annotation.fasta_source.fasta
0
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12 #else
2
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13 #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
0
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14 #end if
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15 #end if
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16 chira_extract.py
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17 -l '$loci'
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18 #if str($annotation.annot_choice) == "yes":
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19 -g '$annotation.gtf'
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20 #if $hybridize:
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21 -f '$genomic_fasta'
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22 #end if
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23 #end if
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24 -tc '$tpm_cutoff'
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25 -sc '$score_cutoff'
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26 -co '$chimeric_overlap'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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27 #if str($reference.ref_type) == "single":
5
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28 -f1 '$reference.ref_fasta'
0
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29 #else if str($reference.ref_type) == "split":
5
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30 -f1 '$reference.ref_fasta1'
dea6bc47a47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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31 -f2 '$reference.ref_fasta2'
dea6bc47a47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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32 #end if
1
de66a3316735 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
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33 $hybridize
9
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34 $seed_interaction
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35 -sbp '$seed_bp'
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36 -smpu '$seed_min_pu'
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37 -acc '$accessibility'
a618f28e1496 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
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38 -accw '$acc_width'
a618f28e1496 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
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39 -m '$intarna_mode'
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40 $summarize
0
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41 -p "\${GALAXY_SLOTS:-2}"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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42 -o ./
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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43 ]]></command>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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44
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45 <inputs>
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46 <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>
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47 <conditional name="annotation">
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48 <param name="annot_choice" type="select" label="Have genomic information?"
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49 help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
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50 <option value="yes">Yes</option>
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51 <option value="no">No</option>
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52 </param>
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53 <when value="yes">
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54 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
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55 <conditional name="fasta_source">
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56 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
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57 <option value="history" selected="true">History</option>
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58 <option value="preloaded">Server indexed files</option>
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59 </param>
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60 <when value="history">
2
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61 <param name="fasta" type="data" format="fasta" label="Genomic FASTA file" />
0
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62 </when>
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63 <when value="preloaded">
2
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64 <param name="fasta_id" type="select" label="Select FASTA index">
0
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65 <options from_data_table="fasta_indexes" />
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66 </param>
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67 </when>
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68 </conditional>
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69 </when>
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70 <when value="no">
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71 <!-- Do nothing -->
5
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72 </when>
0
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73 </conditional>
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74 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
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75 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
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76 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
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77 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
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78 <param name="chimeric_overlap" type="integer" value="2"
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79 label=" Maximum number of bases allowed between the chimericsegments of a read"/>
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80 <conditional name="reference">
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81 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
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82 <option value="split">Split reference</option>
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83 <option value="single">Single reference</option>
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84 </param>
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85 <when value="split">
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86 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
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87 help="Reference fasta file"/>
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88 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
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89 help="Second reference fasta file."/>
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90 </when>
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91 <when value="single">
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92 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
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93 help="Reference fasta file"/>
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94 </when>
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95 </conditional>
9
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96 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
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97 label="Hybridize chimeric loci?"
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98 help="Turning this option on increases the run time of the tool significantly."/>
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99 <param name="intarna_mode" type="select">
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100 <option value="H">Heuristic</option>
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101 <option value="M">Exact</option>
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102 <option value="S">Seed-only</option>
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103 </param>
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104 <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="true"
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105 label="Enforce seed interaction?"/>
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106 <param name="seed_bp" type="integer" value="5" min="2" max="20"
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107 label="Number of inter-molecular base pairs within the seed region"
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108 help="IntaRNA --seedBP parameter"/>
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109 <param name="seed_min_pu" type="float" value="0" min="0" max="1"
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110 label="Minimal unpaired probability (per sequence) a seed region may have"
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111 help="IntaRNA --seedMinPu parameter"/>
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112 <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
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113 label="Compute accessibility profiles for interacting sequences?"/>
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114 <param name="acc_width" type="integer" value="150" min="0" max="99999"
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115 label="Sliding window size for accessibility computation"
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116 help="IntaRNA --accW parameter"/>
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117 <param name="temperature" type="float" value="37" min="0" max="100"
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118 label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
9
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119 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
10
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120 label="Summarize interactions at loci level?"/>
0
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121 </inputs>
5
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122
0
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123 <outputs>
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124 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
9
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125 <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
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126 <filter>summarize == True</filter>
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127 </data>
0
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128 </outputs>
5
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129
0
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130 <tests>
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131 <test expect_num_outputs="2">
0
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132 <param name="loci" value="loci.counts"/>
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133 <param name="ref_type" value="split"/>
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134 <param name="ref_fasta1" value="ref1.fasta"/>
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135 <param name="ref_fasta2" value="ref2.fasta"/>
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136 <param name="annot_choice" value="no"/>
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137 <param name="hybridize" value="true" />
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138 <param name="summarize" value="true" />
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139 <output name="chimeras" file="chimeras"/>
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140 <output name="interactions" file="interactions"/>
0
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141 </test>
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142 </tests>
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143 <help>
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144
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145 .. class:: infomark
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146
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147 **What it does**
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148
5
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149 This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
0
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150
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151 **Inputs**
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152
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153 * Tabular file containing CRLs information
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154 * Annotation GTF file
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155 * Reference fasta files. Provide both in case of split reference.
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156 * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.
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157
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158 **Output**
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159
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160 * Tabular file containing chimeras information
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161 </help>
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162 <expand macro="citations" />
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163 </tool>
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164