Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 16:3233451a3bd6 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
| author | rmarenco |
|---|---|
| date | Sun, 25 Sep 2016 11:25:38 -0400 |
| parents | 2a45cd656e8e |
| children | c02720d1afee |
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--- a/hubArchiveCreator.xml Fri Sep 02 15:41:51 2016 -0400 +++ b/hubArchiveCreator.xml Sun Sep 25 11:25:38 2016 -0400 @@ -12,6 +12,7 @@ <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> <requirement type="package" version="332">ucsc-twobitinfo</requirement> <requirement type="package" version="1.3">samtools</requirement> <!-- ToolShed dependencies --> @@ -60,33 +61,46 @@ #end def #for $i, $f in enumerate( $format ) + #set track_color = str($f.formatChoice.track_color) + #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}) + #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) + #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) + #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i, + {"track_color": $track_color}) #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) + #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) + #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) + #silent $prepare_json($f.formatChoice.GTF, $i, + {"track_color": $track_color}) #end if #end for @@ -130,6 +144,7 @@ <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> @@ -142,30 +157,14 @@ type="data" label="BAM File" /> - </when> - <when value="bigwig"> - <param - format="bigwig" - name="BIGWIG" - type="data" - label="BIGWIG File" - /> - </when> - <when value="gff3"> - <param - format="gff3" - name="GFF3" - type="data" - label="GFF3 File" - /> - </when> - <when value="gtf"> - <param - format="gtf" - name="GTF" - type="data" - label="GTF 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"> @@ -180,6 +179,7 @@ type="data" label="Generic Bed File Choice" /> + </when> <when value="bed_simple_repeats_option"> <param @@ -190,6 +190,73 @@ /> </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>