Mercurial > repos > greg > ideas_genome_tracks
changeset 76:a3bd0cecdeb2 draft
Uploaded
author | greg |
---|---|
date | Wed, 03 Jan 2018 13:59:09 -0500 |
parents | d9342dc571e5 |
children | 8c4549f123da |
files | ideas_genome_tracks.xml |
diffstat | 1 files changed, 28 insertions(+), 24 deletions(-) [+] |
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--- a/ideas_genome_tracks.xml Tue Jan 02 10:53:05 2018 -0500 +++ b/ideas_genome_tracks.xml Wed Jan 03 13:59:09 2018 -0500 @@ -10,8 +10,8 @@ #import re #set dbkey = None #set sanitized_hub_name = $re.sub('\s+', '', str($hub_name), flags=re.UNICODE) -#set sanitized_long_label = str($long_label)[:79] -#set sanitized_short_label = str($short_label)[:16] +#set sanitized_hub_long_label = str($hub_long_label)[:79] +#set sanitized_hub_short_label = str($hub_short_label)[:16] #if str($__user__.email) == 'None': ## This is needed only if the user is not logged in. #set email = "foo@bar.net" @@ -20,12 +20,12 @@ #end if #set input_dir_para = "input_dir_para" #set input_dir_state = "input_dir_state" -#set select_state_color = $select_state_color_cond.select_state_color -#if str($select_state_color) == 'yes': - #set state_color_repeat = $select_state_color_cond.state_color_repeat +#set set_state_name_and_color = $set_state_name_and_color_cond.set_state_name_and_color +#if str($set_state_name_and_color) == 'yes': + #set state_repeat = $set_state_name_and_color_cond.state_repeat #set state_indexes = list() #set state_colors = list() - #for $items in $state_color_repeat: + #for $items in $state_repeat: $state_indexes.append(str($items.state_index)) $state_colors.append(str($items.state_color)) #end for @@ -55,14 +55,15 @@ --hub_name '$hub_name' --input_dir_para '$input_dir_para' --input_dir_state '$input_dir_state' ---long_label '$sanitized_long_label' +--hub_long_label '$sanitized_hub_long_label' --output_trackhub '$output_trackhub' --output_trackhub_files_path '$output_trackhub.files_path' --output_trackhub_id '$__app__.security.encode_id($output_trackhub.id)' --script_dir '$__tool_directory__' ---short_label '$sanitized_short_label' -#if str($select_state_color) == 'yes': +--hub_short_label '$sanitized_hub_short_label' +#if str($set_state_name_and_color) == 'yes': --state_indexes '$state_indexes' + --state_names '$state_names' --state_colors '$state_colors' #end if &>ideas_genome_tracks.log; @@ -74,30 +75,33 @@ <inputs> <param name="galaxy_url" type="baseurl" value="/"/> <param name="input" format="txt" type="data_collection" collection_type="list" label="IDEAS files"/> - <conditional name="select_state_color_cond"> - <param name="select_state_color" type="select" label="Select colors for one or more states?"> + <param name="hub_name" type="text" value="" label="Hub name" help="All white space characters will be eliminated"> + <validator type="empty_field"/> + </param> + <param name="hub_short_label" type="text" value="short label" label="Hub short label" help="Limit to 17 characters"> + <validator type="empty_field"/> + </param> + <param name="hub_long_label" type="text" value="long label" label="Hub long label" help="Limit to 80 characters"> + <validator type="empty_field"/> + </param> + <conditional name="set_state_name_and_color_cond"> + <param name="set_state_name_and_color" type="select" label="Specify names and colors for one or more states?"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no" /> <when value="yes"> - <repeat name="state_color_repeat" title="state color" min="1"> - <param name="state_index" type="integer" value="" min="1" label="State index" help="Enter the integer index of the desired state"> + <repeat name="state_repeat" title="Name and color" min="1"> + <param name="state_index" type="integer" value="" min="0" label="State index" help="Enter the integer index of the state displayed in the IDEAS heatmap"> + <validator type="empty_field"/> + </param> + <param name="state_name" type="text" value="use state index" label="State name" help="The default string 'use state index' sets the name to the state index value"> <validator type="empty_field"/> </param> <param name="state_color" type="color" label="State color"/> </repeat> </when> </conditional> - <param name="hub_name" type="text" value="" label="Hub name" help="All white space characters will be eliminated"> - <validator type="empty_field"/> - </param> - <param name="short_label" type="text" value="short label" label="Short label" help="Limit to 17 characters"> - <validator type="empty_field"/> - </param> - <param name="long_label" type="text" value="long label" label="Long label" help="Limit to 80 characters"> - <validator type="empty_field"/> - </param> </inputs> <outputs> <data name="output_trackhub" format="trackhub"/> @@ -113,8 +117,8 @@ </collection> </param> <param name="hub_name" value="MyHub"/> - <param name="short_label" value="my short label"/> - <param name="long_label" value="my long label"/> + <param name="hub_short_label" value="my short label"/> + <param name="hub_long_label" value="my long label"/> <output name="output_trackhub" file="output_trackhub.html" ftype="trackhub"/> </test> </tests>