Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 24:fcc1021bd496 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
| author | yating-l |
|---|---|
| date | Wed, 31 May 2017 11:35:16 -0400 |
| parents | 2677f1899aa8 |
| children | df42241d3731 |
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--- a/hubArchiveCreator.xml Tue May 09 15:42:43 2017 -0400 +++ b/hubArchiveCreator.xml Wed May 31 11:35:16 2017 -0400 @@ -5,8 +5,10 @@ </description> <requirements> - <requirement type="package" version="1.0">ucsc_tools_340</requirement> + <requirement type="package" version="340">ucsc_hac</requirement> <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="340">ucsc_bigwig</requirement> + <requirement type="package" version="340">ucsc_bigbed</requirement> </requirements> <stdio> @@ -90,6 +92,11 @@ #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, extra_data_dict) #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" + --cytoBand $f.formatChoice.bedChoice.BED_cytoBand + #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, + 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, $index_track_final, @@ -102,12 +109,12 @@ #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment - #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, + #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment - #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, + #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, extra_data_dict) #end if #end if @@ -121,6 +128,11 @@ #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, extra_data_dict) #end if + #if $f.formatChoice.format_select == "bigbed" + --bigbed $f.formatChoice.BIGBED + #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final, + extra_data_dict) + #end if #if $f.formatChoice.format_select == "gff3" --gff3 $f.formatChoice.GFF3 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, @@ -180,6 +192,7 @@ <option value="bed">BED</option> <option value="psl">PSL</option> <option value="bigwig">BIGWIG</option> + <option value="bigbed">BIGBED</option> <option value="gff3">GFF3</option> <option value="gtf">GTF</option> </param> @@ -200,11 +213,12 @@ </valid> </sanitizer> </param> - </when> + </when> <when value="bed"> <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> <option value="bed_generic" selected="true">BED Generic (bed3+)</option> + <option value="bed_cytoBand">cytoBand Track (bed4)</option> <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> @@ -219,6 +233,14 @@ /> </when> + <when value="bed_cytoBand"> + <param + format="bed" + name="BED_cytoBand" + type="data" + label="cytoBand Track (Bed4)" + /> + </when> <when value="bed_simple_repeats_option"> <param format="bed" @@ -293,6 +315,22 @@ </sanitizer> </param> </when> + <when value="bigbed"> + <param + format="bigbed" + name="BIGBED" + type="data" + label="BIGBED File" + /> + <param name="longLabel" type="text" size="30" label="Track name" /> + <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" @@ -474,7 +512,7 @@ /> </output> </test> - + <!-- Test with Psl --> <test> @@ -1029,4 +1067,8 @@ This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </help> + + <citations> + <citation type="doi">10.7490/f1000research.1112719.1</citation> + </citations> </tool>