Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 17:c02720d1afee draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
| author | rmarenco |
|---|---|
| date | Fri, 30 Sep 2016 15:14:24 -0400 |
| parents | 3233451a3bd6 |
| children | d786bca6a75d |
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--- a/hubArchiveCreator.xml Sun Sep 25 11:25:38 2016 -0400 +++ b/hubArchiveCreator.xml Fri Sep 30 15:14:24 2016 -0400 @@ -12,7 +12,8 @@ <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> <requirement type="package" version="332">ucsc-gff3togenepred</requirement> <requirement type="package" version="332">ucsc-gtftogenepred</requirement> - <requirement type="package" version="332">ucsc-psltobigpsl</requirement> + <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before --> + <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> --> <requirement type="package" version="332">ucsc-twobitinfo</requirement> <requirement type="package" version="1.3">samtools</requirement> <!-- ToolShed dependencies --> @@ -21,6 +22,7 @@ <requirement type="package" version="0.0.1">gtfToGenePred</requirement> <requirement type="package" version="0.0.1">genePredToBed</requirement> <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement> + <requirement type="package" version="0.0.1">pslToBigPsl</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> @@ -60,48 +62,59 @@ #end def - #for $i, $f in enumerate( $format ) - #set track_color = str($f.formatChoice.track_color) + #for $i_g, $g in enumerate( $group ) + #for $i, $f in enumerate( $g.format ) + + ## For each format, we have a few mandatory fields we store in a dict + #set track_color = str($f.formatChoice.track_color) + #set group_name = str($g.group_name) - #if $f.formatChoice.format_select == "bam" - --bam $f.formatChoice.BAM - #set bam_index = $f.formatChoice.BAM.metadata.bam_index - #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index, - "track_color": $track_color}) - #end if - #if $f.formatChoice.format_select == "bed" - #if $f.formatChoice.bedChoice.bed_select == "bed" - --bed $f.formatChoice.bedChoice.BED - #silent $prepare_json($f.formatChoice.bedChoice.BED, $i, - {"track_color": $track_color}) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" - --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats - #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i, - {"track_color": $track_color}) + #set extra_data_dict = {"track_color": $track_color, + "group_name": $group_name} + + #if $f.formatChoice.format_select == "bam" + --bam $f.formatChoice.BAM + #set bam_index = $f.formatChoice.BAM.metadata.bam_index + + ## Add Bam format specific fields + #silent extra_data_dict.update({"index": $bam_index}) + + #silent $prepare_json($f.formatChoice.BAM, $i, extra_data_dict) #end if - #end if - #if $f.formatChoice.format_select == "psl" - --psl $f.formatChoice.PSL - #silent $prepare_json($f.formatChoice.PSL, $i, - {"track_color": $track_color}) - #end if - #if $f.formatChoice.format_select == "bigwig" - --bigwig $f.formatChoice.BIGWIG - #silent $prepare_json($f.formatChoice.BIGWIG, $i, - {"track_color": $track_color}) - #end if - #if $f.formatChoice.format_select == "gff3" - --gff3 $f.formatChoice.GFF3 - #silent $prepare_json($f.formatChoice.GFF3, $i, - {"track_color": $track_color}) - #end if - #if $f.formatChoice.format_select == "gtf" - ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 - --gtf $f.formatChoice.GTF - #silent $prepare_json($f.formatChoice.GTF, $i, - {"track_color": $track_color}) - #end if + #if $f.formatChoice.format_select == "bed" + #if $f.formatChoice.bedChoice.bed_select == "bed" + --bed $f.formatChoice.bedChoice.BED + #silent $prepare_json($f.formatChoice.bedChoice.BED, $i, + extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" + --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats + #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i, + extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == "psl" + --psl $f.formatChoice.PSL + #silent $prepare_json($f.formatChoice.PSL, $i, + extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigwig" + --bigwig $f.formatChoice.BIGWIG + #silent $prepare_json($f.formatChoice.BIGWIG, $i, + extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gff3" + --gff3 $f.formatChoice.GFF3 + #silent $prepare_json($f.formatChoice.GFF3, $i, + extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gtf" + ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 + --gtf $f.formatChoice.GTF + #silent $prepare_json($f.formatChoice.GTF, $i, + extra_data_dict) + #end if + #end for #end for ## We combine the fasta file dataset name with his false path in a JSON object @@ -139,126 +152,129 @@ type="data" label="Reference genome" /> - <repeat name="format" title="Formats"> - <conditional name="formatChoice"> - <param name="format_select" type="select" label="Format"> - <option value="bam" selected="true">BAM</option> - <option value="bed">BED</option> - <option value="psl">PSL</option> - <option value="bigwig">BIGWIG</option> - <option value="gff3">GFF3</option> - <option value="gtf">GTF</option> - </param> - - <when value="bam"> - <param - format="bam" - name="BAM" - type="data" - label="BAM File" - /> - <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> - <when value="bed"> - <conditional name="bedChoice"> - <param name="bed_select" type="select" label="Bed Choice"> - <option value="bed" selected="true">BED Generic (bed3+)</option> - <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> - </param> - <when value="bed"> - <param - format="bed" - name="BED" - type="data" - label="Generic Bed File Choice" - /> - - </when> - <when value="bed_simple_repeats_option"> - <param - format="bed" - name="BED_simple_repeats" - type="data" - label="Bed Simple Repeats (Bed4+12) File" - /> - </when> - </conditional> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> + <repeat name="group" title="New group"> + <param type="text" name="group_name" label="Group name" value="Default group"/> + <repeat name="format" title="New track"> + <conditional name="formatChoice"> + <param name="format_select" type="select" label="Format"> + <option value="bam" selected="true">BAM</option> + <option value="bed">BED</option> + <option value="psl">PSL</option> + <option value="bigwig">BIGWIG</option> + <option value="gff3">GFF3</option> + <option value="gtf">GTF</option> </param> - </when> - <when value="psl"> - <param - format="psl" - name="PSL" - type="data" - label="PSL File" - /> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> - <when value="bigwig"> - <param - format="bigwig" - name="BIGWIG" - type="data" - label="BIGWIG File" - /> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> - <when value="gff3"> - <param - format="gff3" - name="GFF3" - type="data" - label="GFF3 File" - /> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> - <when value="gtf"> - <param - format="gtf" - name="GTF" - type="data" - label="GTF File" - /> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> - </conditional> + + <when value="bam"> + <param + format="bam" + name="BAM" + type="data" + label="BAM File" + /> + <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bed"> + <conditional name="bedChoice"> + <param name="bed_select" type="select" label="Bed Choice"> + <option value="bed" selected="true">BED Generic (bed3+)</option> + <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> + </param> + <when value="bed"> + <param + format="bed" + name="BED" + type="data" + label="Generic Bed File Choice" + /> + + </when> + <when value="bed_simple_repeats_option"> + <param + format="bed" + name="BED_simple_repeats" + type="data" + label="Bed Simple Repeats (Bed4+12) File" + /> + </when> + </conditional> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="psl"> + <param + format="psl" + name="PSL" + type="data" + label="PSL File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bigwig"> + <param + format="bigwig" + name="BIGWIG" + type="data" + label="BIGWIG File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gff3"> + <param + format="gff3" + name="GFF3" + type="data" + label="GFF3 File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gtf"> + <param + format="gtf" + name="GTF" + type="data" + label="GTF File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> </repeat> <conditional name="advanced_options"> <param name="advanced_options_selector" type="select" label="Advanced options">