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1 <tool id="emsar" name="EMSAR" version="1.2j">
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2 <description></description>
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3
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4 <command>
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5
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6 #set rsh_path = $refIndex.fields.rshPath
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7 #set rsh = $rsh_path + "." + $nRL.__str__() + ".rsh"
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8 #set libType = ""
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9
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10 #if $bPaired
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11 #if $sLT.__str__() == "n"
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12 #set libType = "ns"
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13 #end if
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14 #if $sLT.__str__() == "f"
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15 #set libType = "ssfr"
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16 #end if
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17 #if $sLT.__str__() == "r"
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18 #set libType = "ssrf"
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19 #end if
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20 #else
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21 #if $sLT.__str__() == "n"
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22 #set libType = "ns"
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23 #end if
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24 #if $sLT.__str__() == "f"
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25 #set libType = "ssf"
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26 #end if
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27 #if $sLT.__str__() == "r"
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28 #set libType = "ssr"
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29 #end if
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30 #end if
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31
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32 emsar
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33 -P
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34 #if $sBS.__str__() == "S"
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35 -S
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36 #end if
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37 #if $sBS.__str__() == "B"
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38 -B
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39 #end if
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40 -p 8
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41 -h $sHT
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42 #if $bG
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43 -g
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44 #end if
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45 -s $libType
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46 -I $rsh
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47 output
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48 emsar
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49 $input_bam
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50 2> emsar.log
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51
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52 </command>
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53
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54 <stdio></stdio>
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55
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56 <inputs>
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57 <param format="bam,sam" compression="none" name="input_bam" type="data" label="Bowtie Alignment BAM file" help=""/>
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58 <param name="refIndex" type="select" label="Select a reference genome" help="">
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59 <options from_data_table="emsar_indices">
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60 <filter type="sort_by" column="2"/>
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61 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
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62 </options>
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63 </param>
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64 <param name="sBS" type="select" label="Input alignment file type ">
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65 <option value="S">SAM</option>
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66 <option value="B">BAM</option>
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67 </param>
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68 <param name="sHT" type="select" label="Transcriptome header type">
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69 <option value="R">RefSeq</option>
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70 <option value="E">Ensembl</option>
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71 </param>
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72 <param name="bG" type="boolean" label="Generate list of all segments with their associated sequence-sharing set and transcript(seperated by '+')" value="True" />
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73 <param name="bPaired" type="boolean" label="Is this paired-end sequenced data ?" value="True" />
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74 <param name="nRL" type="integer" label="read length" value="101" />
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75 <param name="sLT" type="select" label="library type">
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76 <option value="n">Unstranded</option>
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77 <option value="f">Forward Stranded</option>
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78 <option value="r">Reverse Stranded</option>
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79 </param>
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80 </inputs>
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81
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82 <outputs>
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83 <data format="txt" name="fpkm" label="${tool.name} on ${on_string}: FPKM" from_work_dir="output/emsar.0.fpkm" />
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84 <data format="txt" name="fraglength_stat" label="${tool.name} on ${on_string}: Fracgment Length Effect" from_work_dir="output/emsar.0.fraglength_effect" />
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85 <data format="txt" name="segments" label="${tool.name} on ${on_string}: Segments" from_work_dir="output/emsar.0.segments" />
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86 </outputs>
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87
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88 <help>
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89
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90 </help>
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91 </tool>
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