Mercurial > repos > yating-l > hubarchivecreatortest

comparison hubArchiveCreator.xml @ 3:fa990284327b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Mon, 30 Oct 2017 11:58:31 -0400
parents 85195e0d4b71
children
comparison
equal deleted inserted replaced
2:7486909dfc22 3:fa990284327b
121 #end if 121 #end if
122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
123 #set database = str($f.formatChoice.bedChoice.database) 123 #set database = str($f.formatChoice.bedChoice.database)
124 #silent $extra_data_dict.update({"database": $database}) 124 #silent $extra_data_dict.update({"database": $database})
125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" 125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
126 #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) 126 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
127 #silent $extra_data_dict.update({"trix_id": $trix_id}) 127 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
128 #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection"
129 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix)
130 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx)
131 #else
132 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix)
133 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx)
134 #end if
135 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) 128 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
136 #end if 129 #end if
137 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 130 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
138 $extra_data_dict) 131 $extra_data_dict)
139 #end if 132 #end if
140 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" 133 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
141 #set database = str($f.formatChoice.bedChoice.database) 134 #set database = str($f.formatChoice.bedChoice.database)
142 #silent $extra_data_dict.update({"database": $database}) 135 #silent $extra_data_dict.update({"database": $database})
143 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" 136 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
144 #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) 137 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
145 #silent $extra_data_dict.update({"trix_id": $trix_id}) 138 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
146 #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection"
147 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix)
148 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx)
149 #else
150 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix)
151 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx)
152 #end if
153 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) 139 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
154 #end if 140 #end if
155 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 141 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
156 $extra_data_dict) 142 $extra_data_dict)
157 #end if 143 #end if
164 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, 150 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
165 $extra_data_dict) 151 $extra_data_dict)
166 #end if 152 #end if
167 #if $f.formatChoice.format_select == "bigbed" 153 #if $f.formatChoice.format_select == "bigbed"
168 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" 154 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
169 #set trix_id = str($f.formatChoice.add_trix_index.trix_id) 155 #set ix_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ix)
170 #silent $extra_data_dict.update({"trix_id": $trix_id}) 156 #set ixx_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
171 #if $f.formatChoice.add_trix_index.index_files.index_files_type == "collection" 157 #set trix_id = str($f.formatChoice.add_trix_index.add_trix_file.trix_id)
172 #set ix_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ix) 158 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
173 #set ixx_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ixx)
174 #else
175 #set ix_index = str($f.formatChoice.add_trix_index.index_files.index_ix)
176 #set ixx_index = str($f.formatChoice.add_trix_index.index_files.index_ixx)
177 #end if
178 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
179 #end if 159 #end if
180 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, 160 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
181 $extra_data_dict) 161 $extra_data_dict)
182 #end if 162 #end if
183 #if $f.formatChoice.format_select == "gff3" 163 #if $f.formatChoice.format_select == "gff3"
375 name="BIGBED" 355 name="BIGBED"
376 type="data" 356 type="data"
377 label="BIGBED File" 357 label="BIGBED File"
378 /> 358 />
379 <expand macro="add_trix_file"> 359 <expand macro="add_trix_file">
380 <expand macro="specify_search_index" /> 360 <param
361 name="trix_id"
362 value="name"
363 type="text"
364 size="30"
365 label="Specify Trix identifier"
366 />
381 </expand> 367 </expand>
382 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> 368 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
383 <param name="track_color" type="color" label="Track color" value="#000000"> 369 <param name="track_color" type="color" label="Track color" value="#000000">
384 <sanitizer> 370 <sanitizer>
385 <valid initial="string.letters,string.digits"> 371 <valid initial="string.letters,string.digits">