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1 <tool id="ceas_sitepro" name="SitePro: Score profile near Intervals" version="0.1.0">
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2 <description>Draw the score profile near a given interval</description>
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3
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3 <version_command>sitepro --version</version_command>
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4 <macros>
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5 <import>ceas_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Failed" />
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10 </stdio>
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11 <command>
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12 sitepro
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13 #if $mode.mode_select == "single"
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14 -w $mode.wfile -b $mode.bfile
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15 #elif $mode.mode_select == "multiwig"
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16 -w $mode.wfile -l $mode.label
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17 #for $m in $mode.more
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18 -w "$m.wig" -l "$m.label"
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19 #end for
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20 -b $mode.bfile
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21 #elif $mode.mode_select == "multibed"
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22 -w $mode.wfile -b $mode.bfile -l $mode.label
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23 #for $m in $mode.more
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24 -b "$m.bfile" -l "$m.label"
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25 #end for
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26 #end if
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27 --span=$span --pf-res=$pfres --name=$name --dump &> $log &&
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28 cat *_dump.txt > $dump
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29 </command>
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30 <inputs>
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31 <param name="name" type="hidden" value="sitepro_out"/>
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32 <conditional name="mode">
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33 <param name="mode_select" type="select" label="Sitepro behaviour mode" force_select="true">
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34 <option value="single"> 1 wiggle vs 1 BED file</option>
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35 <option value="multiwig"> multiple wiggle vs 1 BED</option>
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36 <option value="multibed"> multiple BED vs 1 wiggle</option>
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37 </param>
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38
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39 <when value="single">
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40 <param ftype="wig" name="wfile" type="data" label="Wiggle file"/>
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41 <param ftype="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
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42 </when>
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43
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44 <when value="multiwig">
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45 <param format="wig" name="wfile" type="data" label="Wiggle file"/>
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46 <param name="label" type="text" label="Wiggle label" optional="false" />
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47 <repeat name="more" title="wiggle file">
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48 <param format="wig" name="wig" type="data" label="Select another wiggle file"/>
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49 <param name="label" type="text" label="Wiggle label" optional="false" />
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50 </repeat>
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51 <param format="bed" name="bfile" type="data"
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52 label="BED file"/>
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53 </when>
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54
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55 <when value="multibed">
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56 <param format="bed" name="bfile" type="data" label="BED file(100,000 lines max)"/>
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57 <param name="label" type="text" label="BED label" optional="false" />
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58 <repeat name="more" title="BED file">
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59 <param format="bed" name="bfile" type="data" label="Select another BED file(100,000 lines max)"/>
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60 <param name="label" type="text" label="BED label" optional="false" />
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61 </repeat>
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62 <param format="wig" name="wfile" type="data" label="Wiggle file"/>
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63 </when>
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64
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65 </conditional>
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66
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67 <param name="span" type="integer" label="Span" value="1000">
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68 <validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" />
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69 </param>
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70 <param name="pfres" type="integer" label="Profiling Resolution" value="50">
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71 <validator type="in_range" max="1000" min="10" message="Profiling Resolution is out of range, Profiling Resolution has to be between 10 to 1000" />
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72 </param>
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73 </inputs>
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74 <outputs>
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75 <data name="output" format="pdf" from_work_dir="sitepro_out.pdf"/>
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76 <data name="log" format="txt" label="sitepro job log" />
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77 <data name="dump" format="txt" label="txt file with profiles" />
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78 </outputs>
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79 <tests>
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80 <test maxseconds="3600" name="Sitepro_1">
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81 <param name="mode_select" value="single" />
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82 <param name="wfile" value="treatment.wig" />
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83 <param name="bfile" value="peaks.bed" />
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84 <param name="span" value="1000" />
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85 <param name="pfres" value="50" />
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86 <output name="output" file="sitepro_1/sitepro_1.pdf" />
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87 <output name="output" file="sitepro_1/sitepro_1.log" lines_diff = "200" />
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88 <output name="output" file="sitepro_1/sitepro_1_dump.txt" />
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89 <output name="log">
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90 <assert_contents>
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91 <has_text_matching expression="See sitepro_out.pdf for the graphical result of sitepro" />
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92 </assert_contents>
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93 </output>
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94 </test>
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95 </tests>
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96 <help>
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97 This tool draws the average score profile around given genomic
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98 sites. It's a module in CEAS package which is written by Hyunjin Gene
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99 Shin, published in Bioinformatics (pubmed id:19689956).
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100
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101 .. class:: infomark
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102
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103 **TIP #1:** If your query does not apper in the pulldown menu for BED Files, please convert your interval files to BED format.
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104
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105 .. class:: infomark
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106
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107 **TIP #2:** You can't use multiple BED files *AND* multiple Wiggle files as input.
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108
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109 .. class:: infomark
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110
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111 **TIP #3:** The tool can be used to check the signals of your ChIP
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112 sample around certain regions such as Transcription Start Sites, or
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113 Transcription Factor Binding Sites.
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114
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115 .. class:: warningmark
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116
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117 **NEED IMPROVEMENT**
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118
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119 -----
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120
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121 **Parameters**
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122
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123 - **Sitepro behaviour mode** can only be '1 wiggle file against 1 BED
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124 file', or 'multiple wiggle files against 1 BED file', or '1 wiggle
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125 file against multiple BED files'.
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126 - **Wiggle label** When 'multi wiggle' mode is selected, you need to assign the labels for every wiggle files which will be shown in the final figure.
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127 - **BED label** When 'multi BED' mode is selected, you need to assign the labels for every BED files which will be shown in the final image.
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128 - **Span** is the distance from the center of each BED region in both directions(+/-) (eg, [c - span, c + span], where c is the center of a region).
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129 - **Profiling resolution** is the resolution to bin the scores in the final image.
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130
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131 -----
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132
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133 **script parameter list of Sitepro**
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134
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135 Options:
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136 --version show program's version number and exit
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137 -h, --help Show this help message and exit.
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138 -w WIG, --wig=WIG input WIG file. WARNING: both fixedStep and
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139 variableStep WIG formats are accepted. Multiple WIG
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140 files can be given via -w (--wig) individually (eg -w
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141 WIG1.wig, -w WIG2.wig). WARNING! multiple wig and bed
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142 files are not allowed.
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143 -b BED, --bed=BED BED file of regions of interest. (eg, binding sites or
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144 motif locations) Multiple BED files can be given via
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145 -b (--bed) individually (eg -b BED1.bed -b BED2.bed).
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146 WARNING! multiple wig and bed files are not allowed.
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147 --span=SPAN Span from the center of each BED region in both
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148 directions(+/-) (eg, [c - span, c + span], where c is
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149 the center of a region), default:1000 bp
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150 --pf-res=PF_RES Profiling resolution, default: 50 bp
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151 --dir If set, the direction (+/-) is considered in
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152 profiling. If no strand info given in the BED, this
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153 option is ignored.
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154 --dump If set, profiles are dumped as a TXT file
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155 --name=NAME Name of this run. If not given, the body of the bed
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156 file name will be used,
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157 -l LABEL, --label=LABEL
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158 Labels of the wig files. If given, they are used as
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159 the legends of the plot and in naming the TXT files of
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160 profile dumps; otherwise, the WIG file names will be
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161 used as the labels. Multiple labels can be given via
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162 -l (--label) individually (eg, -l LABEL1 -l LABEL2).
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163 WARNING! The number and order of the labels must be
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164 the same as the WIG files.
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165
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166 -----
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167
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168 **Output**
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169
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170 - **PDF** format file.
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171 - Dumped signals within given intervals in **plain text**.
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172
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173 </help>
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174
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175 </tool>
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