mirror of
https://github.com/galaxyproject/galaxy.git
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452 lines
20 KiB
Mako
452 lines
20 KiB
Mako
<%inherit file="/base.mako"/>
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<%def name="javascripts()">
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${parent.javascripts()}
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${h.js( "jquery.autocomplete", "jquery.tipsy" )}
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<script type="text/javascript">
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$( function() {
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function show_tool_body(title){
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title.parent().show().css('border-bottom-width', '1px');
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title.next().show('fast');
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if ('${hide_fixed_params}'.toLowerCase() == 'true') {
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// show previously hidden parameters
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title.next().children(".form-row").show();
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}
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}
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function hide_tool_body(title){
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title.parent().css('border-bottom-width', '0px');
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title.next().hide('fast');
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}
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function toggle_tool_body(title) {
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if (title.next().is(':visible')){
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hide_tool_body(title);
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}else{
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show_tool_body(title);
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}
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}
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function toggle_multiinput(select) {
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var placeholder;
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if (select.attr('multiple')) {
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$('.multiinput').removeClass('disabled');
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if (select.val()) {
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select.val(select.val()[0]);
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} else {
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select.val($('option:last', select).val());
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}
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select.removeAttr('multiple').removeAttr('size');
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placeholder = 'type to filter';
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} else {
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$('.multiinput').addClass('disabled');
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$('.multiinput', select.closest('.form-row')).removeClass('disabled');
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select.attr('multiple', 'multiple').attr('size', 8);
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placeholder = 'type to filter, [enter] to select all';
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}
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$('input.multiinput-filter', select.parent()).attr(
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'placeholder', placeholder);
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}
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$( "select[refresh_on_change='true']").change( function() {
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$( "#tool_form" ).submit();
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});
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$("div.toolFormTitle").click(function(){
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toggle_tool_body($(this));
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});
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if ('${hide_fixed_params}'.toLowerCase() == 'true') {
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// hide parameters that are not runtime inputs
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$("div.form-row:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
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$("div.toolForm:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
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}
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else {
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// Collapse non-interactive run-workflow panels by default.
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$("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
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}
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$("#show_all_tool_body").click(function(){
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$("div.toolFormTitle").each(function(){
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show_tool_body($(this));
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});
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});
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$("#hide_all_tool_body").click(function(){
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$("div.toolFormTitle").each(function(){
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hide_tool_body($(this));
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});
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});
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$("#new_history_cbx").click(function(){
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$("#new_history_input").toggle(this.checked);
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});
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$('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').each(function(i, s) {
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var select = $(s);
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var new_width = Math.max(200, select.width()) + 20;
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// Find the label for this element.
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select.closest('.form-row').children('label').append(
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$('<span class="icon-button multiinput"></span>').click(function() {
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if ($(this).hasClass('disabled')) return;
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toggle_multiinput(select);
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select.focus();
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}).attr('original-title',
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'Enable/disable selection of multiple input ' +
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'files. Each selected file will have an ' +
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'instance of the workflow.').tipsy({gravity:'s'})
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);
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var filter = $('<input type="text" class="multiinput-filter" ' +
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'placeholder="type to filter">');
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var filter_timeout = false;
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var original_rows = select.find('option');
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var previous_filter = '';
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// Todo: might have to choose keypress, depending on browser
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filter.keydown(function(e) {
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var filter_select = function() {
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var f = $.trim(filter.val());
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var filtered_rows = original_rows;
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if (f.length >= 1) {
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filtered_rows = original_rows.filter(function() {
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return new RegExp(f, 'ig').test($(this).text());
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});
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}
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select.html('');
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select.html(filtered_rows);
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};
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if (e.which == 13) { // 13 = enter key
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e.preventDefault();
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multi = select.attr('multiple');
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if (typeof multi !== 'undefined' && multi !== false) {
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if (!select.find('option:not(:selected)').length) {
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select.find('option').removeAttr('selected');
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} else {
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select.find('option').attr('selected', 'selected');
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}
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}
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return;
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}
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if (filter.val() != previous_filter) {
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if (filter_timeout) clearTimeout(filter_timeout);
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timeout = setTimeout(filter_select, 300);
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previous_filter = filter.val();
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}
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}).width(new_width).css('display', 'block');
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select.after(filter);
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select.width(new_width);
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});
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});
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</script>
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</%def>
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "autocomplete_tagging" )}
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<style type="text/css">
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#new_history_p{
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line-height:2.5em;
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margin:0em 0em .5em 0em;
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}
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#new_history_cbx{
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margin-right:.5em;
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}
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#new_history_input{
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display:none;
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line-height:1em;
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}
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#ec_button_container{
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float:right;
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}
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div.toolForm{
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margin-top: 10px;
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margin-bottom: 10px;
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}
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div.toolFormTitle{
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cursor:pointer;
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}
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.title_ul_text{
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text-decoration:underline;
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}
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.step-annotation {
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margin-top: 0.25em;
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font-weight: normal;
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font-size: 97%;
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}
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.workflow-annotation {
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margin-bottom: 1em;
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}
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</style>
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</%def>
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<%
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from galaxy.tools.parameters import DataToolParameter, RuntimeValue
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from galaxy.jobs.actions.post import ActionBox
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import re
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import colorsys
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import random
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used_accumulator = []
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wf_parms = {}
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for step in steps:
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for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
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if isinstance(v, basestring):
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for rematch in re.findall('\$\{.+?\}', v):
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if rematch[2:-1] not in wf_parms:
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wf_parms[rematch[2:-1]] = ""
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if wf_parms:
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hue_offset = 1.0 / len(wf_parms)
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hue = 0.0
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for k in wf_parms.iterkeys():
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wf_parms[k] = "#%X%X%X" % tuple([int(x * 255) for x in colorsys.hsv_to_rgb(hue, .1, .9)])
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hue += hue_offset
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%>
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<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
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%if other_values is None:
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<% other_values = values %>
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%endif
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%for input_index, input in enumerate( inputs.itervalues() ):
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%if input.type == "repeat":
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<div class="repeat-group">
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<div class="form-title-row"><b>${input.title_plural}</b></div>
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<% repeat_values = values[input.name] %>
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%for i in range( len( repeat_values ) ):
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%if input.name in errors:
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<% rep_errors = errors[input.name][i] %>
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%else:
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<% rep_errors = dict() %>
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%endif
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<div class="repeat-group-item">
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<% index = repeat_values[i]['__index__'] %>
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<div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
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${do_inputs( input.inputs, repeat_values[ i ], rep_errors, prefix + input.name + "_" + str(index) + "|", step, other_values, already_used )}
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## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div>
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</div>
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%endfor
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## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_add" value="Add new ${input.title}" /></div>
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</div>
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%elif input.type == "conditional":
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<% group_values = values[input.name] %>
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<% current_case = group_values['__current_case__'] %>
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<% new_prefix = prefix + input.name + "|" %>
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<% group_errors = errors.get( input.name, {} ) %>
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${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step, already_used )}
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${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used )}
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%else:
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${row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used )}
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%endif
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%endfor
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</%def>
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<%def name="row_for_param( param, value, other_values, error_dict, prefix, step, already_used )">
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## -- ${param.name} -- ${step.state.inputs} --
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%if error_dict.has_key( param.name ):
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<% cls = "form-row form-row-error" %>
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%else:
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<% cls = "form-row" %>
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%endif
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<div class="${cls}">
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<label>${param.get_label()}</label>
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<div>
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%if isinstance( param, DataToolParameter ):
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%if ( prefix + param.name ) in step.input_connections_by_name:
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<%
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conn = step.input_connections_by_name[ prefix + param.name ]
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%>
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Output dataset '${conn.output_name}' from step ${int(conn.output_step.order_index)+1}
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%else:
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## FIXME: Initialize in the controller
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<%
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if value is None:
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value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
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if not enable_unique_defaults:
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del already_used[:]
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%>
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%if step.type == 'data_input':
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##Input Dataset Step, wrap for multiinput.
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<span class='multiinput_wrap'>
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${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
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</span>
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%else:
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${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
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%endif
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<input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" />
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%endif
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%elif isinstance( value, RuntimeValue ) or ( str(step.id) + '|__runtime__' + prefix + param.name ) in incoming:
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## On the first load we may see a RuntimeValue, so we write
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## an input field using the initial value for the param.
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## Subsequents posts will no longer have the runtime value
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## (since an actualy value will be posted) so we add a hidden
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## field so we know to continue drawing form for this param.
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## FIXME: This logic shouldn't be in the template. The
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## controller should go through the inputs on the first
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## load, fill in initial values where needed, and mark
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## all that are runtime modifiable in some way.
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<%
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value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
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if not enable_unique_defaults:
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del already_used[:]
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%>
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${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
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<input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" />
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%else:
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<%
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p_text = param.value_to_display_text( value, app )
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replacements = []
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if isinstance(p_text, basestring):
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for rematch in re.findall('\$\{.+?\}', p_text):
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replacements.append('wf_parm__%s' % rematch[2:-1])
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p_text = p_text.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
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%>
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%if replacements:
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<span style="display:none" class="parm_wrap ${' '.join(replacements)}">
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${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
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</span>
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<span class="p_text_wrapper">${p_text}</span>
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<input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" />
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%else:
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${param.value_to_display_text( value, app )}
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%endif
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%endif
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</div>
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%if step.upgrade_messages and param.name in step.upgrade_messages:
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<div class="warningmark">${step.upgrade_messages[param.name]}</div>
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%endif
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%if error_dict.has_key( param.name ):
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<div style="color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
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<div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${error_dict[param.name]}</span></div>
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</div>
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%endif
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<div style="clear: both"></div>
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</div>
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</%def>
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<div id='ec_button_container'>
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<span class="action-button" id="show_all_tool_body">Expand All</span>
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<span class="action-button" id="hide_all_tool_body">Collapse</span>
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</div>
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<h2>Running workflow "${h.to_unicode( workflow.name )}"</h2>
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%if has_upgrade_messages:
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<div class="warningmessage">
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Problems were encountered when loading this workflow, likely due to tool
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version changes. Missing parameter values have been replaced with default.
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Please review the parameter values below.
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</div>
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%endif
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%if workflow.annotation:
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<div class="workflow-annotation">${workflow.annotation}</div>
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<hr/>
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%endif
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<form id="tool_form" name="tool_form" method="POST">
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## <input type="hidden" name="workflow_name" value="${h.to_unicode( workflow.name ) | h}" />
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%if wf_parms:
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<div class="metadataForm">
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<div class="metadataFormTitle">Workflow Parameters</div>
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<div class="metadataFormBody">
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%for parm in wf_parms:
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<div class='form-row'><label style='width:100px;'>${parm}<input style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
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%endfor
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</div>
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</div>
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<script type="text/javascript">
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// Set the change hooks for workflow parameters.
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$(document).ready(function () {
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$('.wf_parm_input').bind('change keypress keyup', function(event){
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// DBTODO This is probably not reliable. Ensure we have the right class.
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var new_text = $(this).val();
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if (new_text === ''){
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var tag_id = $(this).attr("class").split(' ')[1].substring(5);
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// Set text properly.
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$('.wfpspan.wf_parm__'+tag_id).text(tag_id);
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}else{
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var tag_id = $(this).attr("class").split(' ')[1].substring(5);
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// Set text properly.
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$('.wfpspan.wf_parm__'+tag_id).text(new_text);
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// Now set the hidden input to the generated text.
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$('.wfpspan.wf_parm__'+tag_id).not('.pja_wfp').each(function(){
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var new_text = $(this).parent().text();
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$(this).parent().siblings().children().val(new_text);
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});
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}
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});
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});
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</script>
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%endif
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%for i, step in enumerate( steps ):
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%if step.type == 'tool' or step.type is None:
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<%
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tool = trans.app.toolbox.get_tool( step.tool_id )
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%>
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<input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}">
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<div class="toolForm">
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<div class="toolFormTitle">
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<span class='title_ul_text'>Step ${int(step.order_index)+1}: ${tool.name}</span>
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% if step.annotations:
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<div class="step-annotation">${h.to_unicode( step.annotations[0].annotation )}</div>
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% endif
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</div>
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<div class="toolFormBody">
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${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
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% if step.post_job_actions:
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<hr/>
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<div class='form-row'>
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% if len(step.post_job_actions) > 1:
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<label>Actions:</label>
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% else:
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<label>Action:</label>
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% endif
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<%
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pja_ss_all = []
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for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
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for rematch in re.findall('\$\{.+?\}', pja_ss):
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pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
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pja_ss_all.append(pja_ss)
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%>
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${'<br/>'.join(pja_ss_all)}
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</div>
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% endif
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</div>
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</div>
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%else:
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<% module = step.module %>
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<input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
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<div class="toolForm">
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<div class="toolFormTitle">
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<span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
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% if step.annotations:
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<div class="step-annotation">${step.annotations[0].annotation}</div>
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% endif
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</div>
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<div class="toolFormBody">
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<%
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# Filter possible inputs to data types that are valid for subsequent steps
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type_filter = []
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for oc in step.output_connections:
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for ic in oc.input_step.module.get_data_inputs():
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if 'extensions' in ic and ic['name'] == oc.input_name:
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type_filter += ic['extensions']
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if not type_filter:
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type_filter = ['data']
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%>
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${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
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</div>
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</div>
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%endif
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%endfor
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%if missing_tools:
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<div class='errormessage'>
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<strong>This workflow utilizes tools which are unavailable, and cannot be run. Enable the tools listed below, or <a href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">edit the workflow</a> to correct these errors.</strong><br/>
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<ul>
|
|
%for i, tool in enumerate( missing_tools ):
|
|
<li>${tool}</li>
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|
%endfor
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|
</ul>
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|
%else:
|
|
%if history_id is None:
|
|
<p id='new_history_p'>
|
|
<input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label>
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|
<span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span>
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|
</p>
|
|
%endif
|
|
<input type="submit" name="run_workflow" value="Run workflow" />
|
|
</form>
|
|
%endif
|