Mercurial > repos > vandelj > giant_aptsummarize

annotate galaxy/wrappers/ArrayNormalization.xml @ 2:41f95153ce4b draft default tip

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
author vandelj
date Fri, 25 Sep 2020 08:51:51 +0000
parents 2762a2622e0d
children
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1 <tool name="GIANT-Normalization with APT Summarize" id="giant_aptsummarize" version="0.1.1">
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2 <description>Apply Affymetrix Power Tool summarize function to .CEL collection</description>
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3 <requirements>
1
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4 <requirement type="package" version="2.10.2">apt-probeset-summarize</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="Execution halted"
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8 source="both"
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9 level="fatal"
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10 description="Execution halted, please contact tool developer or administrators." />
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11 <exit_code range="10" level="fatal" description="Error in post-treatments, see log file for more information." />
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12 <exit_code range="1:9" level="fatal" description="Error during apt command execution, see log file for more information." />
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13 </stdio>
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14 <command> <![CDATA[
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15 ##only for local test, comment otherwise
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16 ##set $pathToApt='/mnt/galaxy/home/galaxy/Software/ThermoFischer/apt-1.20.6-x86_64-intel-linux/bin'
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17
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18 mkdir ./apt_output/;
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19
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20 #if $mainCondition.arraySelection=="other":
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21 #if $CDFfile:
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22 ##.cdf file should has original name
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23 cp $CDFfile ./${CDFfile.name};
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24 #end if
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25 #end if
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26
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28 ##run APT command
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29
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30 ##ONLY FOR LOCAL TEST PURPOSE COMMENT IF NOT NECESSARY
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31 ##${pathToApt}/apt-probeset-summarize -a $commandLine
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32 ##AND UNCOMMENT LINE BELOW
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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33 apt-probeset-summarize -a $commandLine
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34
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35 #if $mainCondition.arraySelection=="other":
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36 #if $PGFfile and $CLFfile:
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37 --use-pgf-names
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38 -p $PGFfile
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39 -c $CLFfile
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40 #end if
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41 #if $CDFfile:
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42 -d ./${CDFfile.name}
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43 #end if
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44 #if $MPSfile and $normLevel=="core":
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45 -m $MPSfile
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46 #end if
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47 #if $BGPfile:
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48 -b $BGPfile
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49 #end if
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50
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51 #else:
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52
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53 #if $mainCondition.arrayID.fields.pathPGF!="null" and $mainCondition.arrayID.fields.pathCLF!="null":
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54 --use-pgf-names
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55 -p $mainCondition.arrayID.fields.pathPGF
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56 -c $mainCondition.arrayID.fields.pathCLF
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57 #else:
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58 #if $mainCondition.arrayID.fields.pathCDF!="null":
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59 -d $mainCondition.arrayID.fields.pathCDF
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60 #end if
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61 #end if
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62 #if $normLevel=="core" and $mainCondition.arrayID.fields.pathMPS!="null":
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63 -m $mainCondition.arrayID.fields.pathMPS
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64 #end if
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65 #if $mainCondition.arrayID.fields.pathBGP!="null":
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66 -b $mainCondition.arrayID.fields.pathBGP
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67 #end if
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68 #end if
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69
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70 -o ./apt_output/
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71
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72 \$(echo '$inputData' | tr "," " ") >> $log 2>&1;
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73
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74 ret_code=\$?;
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75
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76 printf "[INFO]Normalized files: "$inputData >> $log;
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77
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78 if [ \$ret_code != 0 ]; then
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79 exit \$ret_code;
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80 else
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81
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82 ##launch post-treatment scripts
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83
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84 bash $scriptFormat;
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85 #if $annotationCondition.addAnnotation=="true":
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86 echo "[INFO]Annotation file used:" >> $log;
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87 #if $mainCondition.arraySelection=="other":
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88 bash $scriptAnnotation $mainCondition.annotationFile;
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89 echo $mainCondition.annotationFile.name >> $log;
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90 #else:
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91 #if $normLevel=="core":
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92 bash $scriptAnnotation $mainCondition.arrayID.fields.pathAnnotTrans;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
93 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
94 bash $scriptAnnotation $mainCondition.arrayID.fields.pathAnnotProbe;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
95 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
96 cat $mainCondition.arrayID.fields.versionInfo >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
97 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
98 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
99 fi;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
100 printf "[INFO]End of tool script" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
101 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
102 </command>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
103
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
104 <configfiles>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
105 <configfile name="scriptFormat">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
106 <![CDATA[
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
107 #for $inputDataset in $inputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
108 echo '${inputDataset.name}' >> ./tempColumnName.txt
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
109 #end for
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
110 awk ' BEGIN{firstLine=1;OFS="";ORS=""} ARGIND==1{tab[FNR]=$1;nbCol=FNR} ARGIND==2 && !($1 ~ /\\#/){if(firstLine==0){print "\n"\$0}else{print "Conditions";for(i=1;i<=nbCol;i++){print "\t"tab[i]};firstLine=0}}' ./tempColumnName.txt ./apt_output/*summary.txt > $outputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
111
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
112 if [ ! -e $outputData ]; then
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
113 printf "[ERROR]Formating results failed" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
114 exit 10
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
115 fi
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
116 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
117 </configfile>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
118
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
119 <configfile name="scriptAnnotation">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
120 <![CDATA[
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
121 #if $annotationCondition.addAnnotation=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
122 #if $annotationCondition.mergingMethod=="none":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
123
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
124 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
125 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0} ARGIND==2 && FNR>1{if(\$1 in dico){\$1=dico[\$1]"_("\$1")";print \$0}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
126 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
127 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0} ARGIND==2 && FNR>1{if(\$1 in dico){\$1=dico[\$1]"_("\$1")"};print \$0}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
128 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
129
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
130 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
131 #if $annotationCondition.mergingMethod=="mean":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
132
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
133 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
134 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){cpt[dico[\$1]]++;for(i=2;i<=nbCol;i++)sum[dico[\$1]][i]+=\$i}} END{for(iName in cpt){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"sum[iName][iCol]/cpt[iName]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
135 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
136 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){cpt[dico[\$1]]++;for(i=2;i<=nbCol;i++)sum[dico[\$1]][i]+=\$i}else{print \$0}} END{for(iName in cpt){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"sum[iName][iCol]/cpt[iName]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
137 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
138
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
139 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
140
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
141 #if $annotationCondition.mergingMethod=="higherVar":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
142
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
143 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
144 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(curVar>var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
145 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
146 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(curVar>var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}else{print \$0}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
147 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
148
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
149 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
150
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
151 #if $annotationCondition.mergingMethod=="lowerVar":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
152
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
153 #if $annotationCondition.keepAnnotated=="true":
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
154 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(var[dico[\$1]]==0 || curVar<var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
155 #else:
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
156 awk 'BEGIN{OFS="\t"} ARGIND==1{dico[\$1]=\$2} ARGIND==2 && FNR==1{print \$0;nbCol=NF} ARGIND==2 && FNR>1{if(\$1 in dico){mean=0;for(i=2;i<=nbCol;i++){mean+=\$i};mean=mean/(nbCol-1);curVar=0;for(i=2;i<=nbCol;i++){curVar+=(mean-\$i)^2};if(var[dico[\$1]]==0 || curVar<var[dico[\$1]]){var[dico[\$1]]=curVar;for(i=2;i<=nbCol;i++){bestVar[dico[\$1]][i]=\$i}}}else{print \$0}} END{for(iName in bestVar){line=iName;for(iCol=2;iCol<=nbCol;iCol++){line=line"\t"bestVar[iName][iCol]};print line}}' \$1 $outputData > ./tempData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
157 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
158
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
159 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
160
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
161 if [ -e ./tempData ]; then
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
162 mv -f ./tempData $outputData
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
163 else
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
164 printf "[ERROR]Annotation merge failed" >> $log;
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
165 exit 10
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
166 fi
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
167
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
168 #end if
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
169
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
170 ]]>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
vandelj
parents:
diff changeset
171 </configfile>
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172 </configfiles>
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173
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174 <inputs>
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175 <param type="text" name="title" value="APT_toPersonalize" label="Title for output"/>
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176
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177 <param type="data" name="inputData" format="cel" label=".cel collection file" optional="false" multiple="true">
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178 <validator type="empty_dataset" message="At least one data file should be selected"></validator>
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179 </param>
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180
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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181 <param type="select" name="commandLine" display="radio" label="Normalization to perform" help="For more details go to APT webpage">
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182 <option value="rma-gc-scale" selected="true">gc correction + scale intensity + rma</option>
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183 <option value="scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish">scale intensity + rma</option>
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184 <option value="gc-correction,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish">gc correction + rma</option>
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185 <option value="rma">rma</option>
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186 </param>
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187
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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188 <param type="select" name="normLevel" display="radio" label="Normalization level" help="'Core genes' option is not available for all arrays">
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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189 <option value="core">Core genes</option>
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190 <option value="probeset">Probe set</option>
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191 </param>
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192
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193 <conditional name="mainCondition">
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194
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195 <param name="arraySelection" type="select" label="Select GeneChip array configuration files">
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196 <option value="common">pre-loaded array files</option>
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197 <option value="other">array files selection</option>
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198 </param>
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199
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200 <when value="common">
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201 <param name="arrayID" label="Name" type="select">
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202 <options from_data_table="aptTool">
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203 </options>
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204 </param>
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205 </when>
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206
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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207 <when value="other">
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208
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209 <param type="data" format="data" name="PGFfile" label=".pgf indicates which probes are grouped together into a probeset*" optional="true" multiple="false">
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210 </param>
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211
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212 <param type="data" format="data" name="CLFfile" label=".clf indicates where the probes are located in the CEL file*" optional="true" multiple="false">
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213 </param>
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214
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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215 <param type="data" format="data" name="CDFfile" label=".cdf contains both .pgf and .clf informations* (requested only if .pgf and .clf files are not available)" optional="true" multiple="false">
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216 </param>
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217
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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218 <param type="data" format="data" name="MPSfile" label=".mps defines a probeset as a collection of existing probesets* (requested for normalization at gene level)" optional="true" multiple="false" help="If .mps is not selected/available a 'probeset level' normalization will be automatically performed">
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219 </param>
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220
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221 <param type="data" format="data" name="BGPfile" label=".bgp indicates which probes are to be used for computing background* (requested only if GC driven background correction is applied)" optional="true" multiple="false" help="*Files should be downloaded from corresponding array specific Affymetrix webpage to insure format compatibility">
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222 </param>
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223
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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224 <param type="data" name="annotationFile" format="tabular" label="tabular file containing available probesets annotation (requested if annotation options are selected)" optional="true" multiple="false" >
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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225 </param>
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226
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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227 </when>
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228 </conditional>
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229
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230 <conditional name="annotationCondition">
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231 <param type="boolean" name="addAnnotation" checked="false" label="Add gene annotation">
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232 </param>
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233 <when value="true">
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234 <param type="boolean" name="keepAnnotated" checked="false" label="Discard probe set without gene annotation">
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235 </param>
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236
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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237 <param type="select" name="mergingMethod" display="radio" label="Merging approach for probe set with same gene annotation">
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238 <option value="none">No merging</option>
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239 <option value="mean" selected="true">Mean between probes [recommended]</option>
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240 <option value="higherVar">Keep probe with higher variance</option>
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241 <option value="lowerVar">Keep probe with lower variance</option>
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242 </param>
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243 </when>
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244 <when value="false">
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245 </when>
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246 </conditional>
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247 </inputs>
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248
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249 <outputs>
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250 <data format="tabular" name="outputData" label="${title}_NormalizedData"/>
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251 <data format="txt" name="log" label="${title}_Log" />
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252 </outputs>
1
2762a2622e0d "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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253
0
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254
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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255
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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256 <tests>
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257 <test maxseconds="3600">
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258 <param name="inputData" value="./CELfiles/GSM205766.CEL,./CELfiles/GSM205767.CEL,./CELfiles/GSM205768.CEL" />
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259 <param name="commandLine" value="rma-gc-scale" />
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260 <param name="normLevel" value="core" />
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261 <param name="arraySelection" value="other" />
1
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262 <param name="CDFfile" value="./APT-summarize/input/Mouse430_2.cdf" />
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263 <param name="annotationFile" value="./APT-summarize/input/formatedAnnotation.csv" />
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264 <param name="addAnnotation" value="true" />
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265 <param name="keepAnnotated" value="false" />
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266 <param name="mergingMethod" value="mean" />
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267 <output name="outputData" file="./APT-summarize/output/outputExpression.csv" />
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268 <output name="log" file="./APT-summarize/output/outputLog.txt" compare="sim_size" delta_frac="0.15" />
0
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269 </test>
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270 </tests>
0
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271
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272
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273
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274 <help>
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275 <![CDATA[
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276 **What it does**
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277
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278 To normalize expression data from Affymetrix GeneChip arrays through Affymetrix Power Tools software.
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279
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280 -----
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281
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282 **Parameters**
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283
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284 \- **Title** to personalize output file names (please avoid special characters).
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285
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286
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287 \- **.CEL files** you want to normalize (you can select multiple .CEL files or unique collection).
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288
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289
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290 \- **Analysis to perform** : as this tool run the 'apt-probeset-summarize' command line from Affymetrix Power Tool software, this field represents the desired analysis pathway (-a parameter). Analysis pathways are summarized through predifined pathway alias with full description of all run steps below:
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291
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292 - gc correction + scale intensity + rma: "gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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293
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294 - scale intensity + rma: "scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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295
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296 - gc correction + rma: "gc-correction,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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297
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298 - rma: "rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish"
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299
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300 Please refer to `APT tool web page`__ to get more details about analysis steps.
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301
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302 \- **Normalization level** to choose when GeneChip array kind allows such distinction (ie. when a .mps file exists in Affymetrix webpage). 'Probe set level' is the first level where probes for same exon are merged in probe sets. 'Gene level' [recommended] is an upper level where several probe sets are merged in meta probe sets. If a meta probe set can be see as a good single gene expression indicator, several meta probe sets can still share same gene annotation.
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303
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304 \- **GeneChip array configuration files** according to .CEL files. Configuration files for given arrays can be pre-loaded by administrators of the used Galaxy instance and listed in the aptTool.loc file. In this case you just have to select the array kind according to .CEL files, thus pre-loaded configuration files will be used automatically for normalization. If configuration files were not pre-loaded, you have to choose "array files selection" and then select manually configuration files for the corresponding array. Configuration files (.pgf, .clf, .cdf, .mps, .bgp) are available in library archive files from the Affymetrix webpage of the array (as an example, configuration files for HTA2.0 array are found in the 'Main Analysis Files' in the 'Support file' section of `this page`__). All these files are not mandatory for all normalizations. For basic normalization, both .pgf and.clf files or only .cdf file are mandatory. .mps file is requested for gene level normalization if it is available (see Normalization level parameter). .bgp file is requested for analysis pathway with specific background computation. Annotation file is a simple two column tabular file, with first column containing probe set names and second corresponding annotations, it should not contains any column header. This file can be generated from Affymetrix annotation file available in the same section as array configuration files in Affymetrix webpages, please keep a trace of used annotation version to insure reproducibility.
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305
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306 Extract of annotation file::
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307
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308 TC01000020.hg.1 SAMD11
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309 TC01000021.hg.1 KLHL17
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310 TC01000022.hg.1 PLEKHN1
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311 TC01000023.hg.1 ISG15
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312 TC01000024.hg.1 AGRN
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313
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314 \- **Gene annotation** : add gene annotation when available (for pre-loaded arrays, annotation file path should be filled in the aptTool.loc file, for other arrays, annotation file should be selected manually). You can choose to keep or discard in normalized file (meta) probe sets without match in annotation file and select merging policy for probe sets sharing same gene annotation.
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315
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316 -----
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317
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318 **Advanced parameters**
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319
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320 \- **Additional parameter** to give to 'apt-probeset-summarize' command line except -a, -o, -d, -p, -c, -m, -b parameters already filled by previous fields.
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321
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322 -----
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323
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324 **Outputs**
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325
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326 \- **tabular file** containing log2 transformed normalized data as tab delimited matrix. First row contains .CEL names and first column contains (meta) probe set names and/or annotated gene names::
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327
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328 Conditions 157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL 155_(HuGene-2_0-st).CEL 154_(HuGene-2_0-st).CEL
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329 DDX11L2 4.500872 4.429759 4.780281 4.996189
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330 MIR1302-2 3.415065 3.520472 3.471503 3.567988
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331 OR4F5 3.737956 3.011586 3.424494 3.497545
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332 VWA1 5.189621 5.129595 4.806793 5.227014
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333
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334 \- **LOG file** containing information about execution. Useful especially if tool execution fais. Please attach this log file in any bug report.
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335
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336 .. __: http://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html#intro
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337
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338 .. __: https://www.thermofisher.com/order/catalog/product/902233#/902233
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339
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340 ]]>
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341 </help>
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342
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343
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344 <citations>
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345 <citation type="bibtex">@misc{vandel_jimmy_2018_1477870, author = {Vandel, J. and Gheeraert, C. and Eeckhoute, J. and Staels, B. and Lefebvre, P. and Dubois-Chevalier, J.}, title = {GIANT: Galaxy-based Interactive tools for ANalaysis of Transcriptomic data}, month = nov, year = 2018, doi = {10.5281/zenodo.1477870}, url = {https://doi.org/10.5281/zenodo.1477870}
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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346 }</citation>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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347
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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348 <citation type="bibtex">@online{apt, author = {Thermo Fisher Scientific}, title = {Affymetrix Power Tools}, publisher = {Life Technologies Corp.}, address = {USA, MA}, version = {2.10.2}, year = {2018}, url = {https://www.affymetrix.com/support/developer/powertools/changelog/index.html}
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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349 }</citation>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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350 </citations>
708f43bda2b6 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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351 </tool>