Mercurial > repos > nilesh > rseqc

annotate rseqc_macros.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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1 <macros>
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2 <token name="@TOOL_VERSION@">5.0.1</token>
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@GALAXY_VERSION@">20.01</token>
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5 <xml name="requirements">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
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34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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8 <yield/>
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9 </requirements>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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10 </xml>
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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11 <xml name="bio_tools">
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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12 <xrefs>
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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13 <xref type="bio.tools">rseqc</xref>
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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14 </xrefs>
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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15 </xml>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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16 <xml name="stdio">
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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17 <stdio>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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18 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
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19 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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20 </stdio>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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21 </xml>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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22
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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23 <!-- Params -->
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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24 <xml name="bam_param">
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25 <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
51
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26 </xml>
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28 <xml name="bam_sam_param">
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29 <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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30 </xml>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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32 <xml name="refgene_param">
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33 <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 </xml>
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35
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36 <xml name="mapq_param">
60
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37 <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30"
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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38 help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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39 </xml>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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41 <xml name="readlength_param">
60
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42 <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/>
51
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43 </xml>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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44
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45 <xml name="readnum_param">
60
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46 <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/>
51
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47 </xml>
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48
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49 <xml name="sample_size_param">
60
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50 <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/>
51
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51 </xml>
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52
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53 <xml name="min_intron_param">
60
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54 <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
51
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55 </xml>
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56
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57 <xml name="layout_param">
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58 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
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59 <option value="SE" selected="true">Single-end</option>
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60 <option value="PE">Paired-end</option>
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61 </param>
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62 </xml>
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63
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64 <xml name="strand_type_param">
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65 <conditional name="strand_type">
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66 <param name="strand_specific" type="select" label="Strand-specific?">
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67 <option value="none" selected="true">None</option>
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68 <option value="pair">Pair-End RNA-seq</option>
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69 <option value="single">Single-End RNA-seq</option>
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70 </param>
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71 <when value="pair">
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72 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)">
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73 <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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74 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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75 </param>
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76 </when>
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77 <when value="single">
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78 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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79 <option value="s" selected="true">positive --> positive; negative --> negative</option>
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80 <option value="d">positive --> negative; negative --> positive</option>
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81 </param>
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82 </when>
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83 <when value="none"></when>
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84 </conditional>
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85 </xml>
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86
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87 <xml name="multihits_param">
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88 <conditional name="multihits_type">
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89 <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
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90 <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
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91 <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
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92 </param>
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93 <when value="skip_multihits">
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94 <expand macro="mapq_param" />
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95 </when>
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96 <when value="use_multihits" />
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97 </conditional>
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98 </xml>
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99
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100 <xml name="rscript_output_param">
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101 <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
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102 help="Output the R-Script used to generate the plots" />
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103 </xml>
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104
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105
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106 <!-- Output -->
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107
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108 <xml name="pdf_output_data" token_filename="output.pdf">
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109 <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
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110 </xml>
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111
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112 <xml name="xls_output_data" token_filename="output.xls">
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113 <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
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114 </xml>
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115
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116 <xml name="rscript_output_data" token_filename="output.r">
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117 <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
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118 <filter>rscript_output</filter>
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119 </data>
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120 </xml>
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121
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122 <!-- Command -->
60
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123 <token name="@MULTIHITS@"><![CDATA[
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124 #if str($multihits_type.multihits_type_selector) == "skip_multihits"
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125 --skip-multi-hits
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126 --mapq=${multihits_type.mapq}
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127 #end if
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128 ]]></token>
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129
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130 <token name="@BAM_SAM_INPUTS@"><![CDATA[
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131 #set $extension = str($input.ext)
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132 ln -s -f '${input}' 'input.${extension}' &&
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133 #if $extension == 'bam'
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134 ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
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135 #end if
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136 ]]></token>
51
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137
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138 <token name="@ABOUT@">
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139
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140 -----
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141
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142 About RSeQC
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143 +++++++++++
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144
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145 The RSeQC_ package provides a number of useful modules that can comprehensively
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146 evaluate high throughput sequence data especially RNA-seq data. "Basic modules"
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147 quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC
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148 bias, while "RNA-seq specific modules" investigate sequencing saturation status
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149 of both splicing junction detection and expression estimation, mapped reads
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150 clipping profile, mapped reads distribution, coverage uniformity over gene
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151 body, reproducibility, strand specificity and splice junction annotation.
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152
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153 The RSeQC package is licensed under the GNU GPL v3 license.
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154
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155 .. image:: $PATH_TO_IMAGES/logo.png
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156
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157 .. _RSeQC: http://rseqc.sourceforge.net/
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158
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159
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160 </token>
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161
49
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162 <xml name="citations">
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163 <citations>
51
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164 <citation type="doi">10.1093/bioinformatics/bts356</citation>
49
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165 </citations>
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166 </xml>
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167 </macros>