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Adding consistent styling to query descriptor labels.

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VelNZ committed Mar 6, 2018
1 parent 6e33237 commit 43368dd3762ed924e1e5b864f4828704938f8cd8
Showing with 42 additions and 31 deletions.
  1. +13 −2 css/style.css
  2. +16 −16 gbs_administration.php
  3. +5 −5 gbs_query.php
  4. +8 −8 query.php
@@ -1057,7 +1057,7 @@
}

/*********************************************************************************/
/* GBS method boxes (Vel added) */
/* GBS method boxes (Vel added) */
/*********************************************************************************/

.gbs_present {
@@ -1074,4 +1074,15 @@
font-size: 80%;
padding:5pt;
color:white;
}
}

/*********************************************************************************/
/* Query page label style */
/*********************************************************************************/

.query_label {
font-size:75%;
line-height: normal;
padding-top: 5px;
}

@@ -173,39 +173,39 @@
echo "<div class=\"8u\">";
echo "<div class=\"selection\" id=\"cnvnator\">";
echo "<input type=\"text\" name=\"import_sample_cnvnator\">";
echo "<p style=\"font-size:75%;\">Enter the sample name CNVnator was run on above.</p>";
echo "<p class=\"query_label\">Enter the sample name CNVnator was run on above.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"sequenza\" style=\"display: none;\">";
echo "<input type=\"text\" name=\"import_sample_sequenza\">";
echo "<p style=\"font-size:75%;\">Enter the sample name Sequenza was run on above.</p>";
echo "<p class=\"query_label\">Enter the sample name Sequenza was run on above.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"purple\" style=\"display: none;\">";
echo "<input type=\"text\" name=\"import_sample_purple\">";
echo "<p style=\"font-size:75%;\">Enter the sample name PURPLE was run on above.</p>";
echo "<p class=\"query_label\">Enter the sample name PURPLE was run on above.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"rohmer\" style=\"display: none;\">";
echo "<input type=\"text\" name=\"import_sample_rohmer\">";
echo "<p style=\"font-size:75%;\">Enter the sample name ROHmer was run on above.</p>";
echo "<p class=\"query_label\">Enter the sample name ROHmer was run on above.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"varpipesv\" style=\"display: none;\">";
echo "<p style=\"color:red; font-size:8pt;\">VarpipeSV contains sample names in the VCF output.</p>";
echo "<p class=\"query_label\" style=\"color:red;\">VarpipeSV contains sample names in the VCF output.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"manta\" style=\"display: none;\">";
echo "<p style=\"color:red; font-size:8pt;\">Manta contains sample names in the VCF output.</p>";
echo "<p class=\"query_label\" style=\"color:red;\">Manta contains sample names in the VCF output.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"lumpy\" style=\"display: none;\">";
echo "<p style=\"color:red; font-size:8pt;\">LUMPY contains sample names in the VCF output.</p>";
echo "<p class=\"query_label\" style=\"color:red;\">LUMPY contains sample names in the VCF output.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"cnvkit\" style=\"display: none;\">";
echo "<input type=\"text\" name=\"import_sample_cnvkit\">";
echo "<p style=\"font-size:75%;\">Enter the sample name CNVkit was run on above.</p>";
echo "<p class=\"query_label\">Enter the sample name CNVkit was run on above.</p>";
echo "</div>";
echo "</div>";
echo "</div>";
@@ -218,35 +218,35 @@
echo "</div>";
echo "<div class=\"selection\" id=\"varpipesv\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the .vcf file.</p>";
echo "<p class=\"query_label\">Select the .vcf file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"rohmer\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the .bed file.</p>";
echo "<p class=\"query_label\">Select the .bed file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"lumpy\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the .vcf file.</p>";
echo "<p class=\"query_label\">Select the .vcf file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"cnvnator\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the .bed file.</p>";
echo "<p class=\"query_label\">Select the .bed file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"sequenza\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the segments.txt file.</p>";
echo "<p class=\"query_label\">Select the segments.txt file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"purple\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the purple.cnv file.</p>";
echo "<p class=\"query_label\">Select the purple.cnv file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"manta\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the somaticSV.vcf file.</p>";
echo "<p class=\"query_label\">Select the somaticSV.vcf file.</p>";
echo "</div>";
echo "<div class=\"selection\" id=\"cnvkit\" style=\"display: none;\">";
echo "<p style=\"font-size:75%;\">Select the .cns file.</p>";
echo "<p class=\"query_label\">Select the .cns file.</p>";
echo "</div>";
echo "<div class=\"row\">";
@@ -418,7 +418,7 @@
$input_search_genes .= "placeholder=\"e.g. BRCA1;PIK3CA;TP53\">";
}
echo $input_search_genes; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple genes with a semicolon, comma or space.</p>";
echo "<p class=\"query_label\">Separate multiple genes with a semicolon, comma or space.</p>";
echo "</div>";
// The sample overlapping blocks selection div
@@ -466,7 +466,7 @@
$input_search_regions .= "placeholder=\"e.g. chr2:15483-25583;chr1:37211-67824;chr5;MT\">";
}
echo $input_search_regions; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple regions to search with a <strong>semicolon</strong>.</p>";
echo "<p class=\"query_label\">Separate multiple regions to search with a <strong>semicolon</strong>.</p>";
echo "</div>";
// The ROHmer selection div
@@ -520,7 +520,7 @@
$input_search_genes .= "placeholder=\"e.g. BRCA1;PIK3CA;TP53\">";
}
echo $input_search_genes; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple genes with a semicolon, comma or space.</p>";
echo "<p class=\"query_label\">Separate multiple genes with a semicolon, comma or space.</p>";
echo "</div>";
#############################################
@@ -560,7 +560,7 @@
echo "<input type=\"range\" name=\"cnlessthan\" id=\"cnlessthan\" min=\"0\" max=\"2\" step=\"0.1\" value=\"".$default_cn_less_than."\" oninput=\"document.querySelector('#cnlessthanvalue').value = value;\">";
echo "<output for=\"cnlessthan\" id=\"cnlessthanvalue\">".$default_cn_less_than."</output>";
echo "<p style=\"font-size:75%; line-height: normal;\">Return deletion variants with a copy number below this value. <strong>To return all deletion variants, set this value to 2.</strong> All variants with no copy number will be returned.</p>";
echo "<p class=\"query_label\">Return deletion variants with a copy number below this value. <strong>To return all deletion variants, set this value to 2.</strong> All variants with no copy number will be returned.</p>";
echo "</section>";
// Greater than
@@ -569,7 +569,7 @@
echo "<input type=\"range\" name=\"cngreaterthan\" id=\"cngreaterthan\" min=\"2\" max=\"15\" step=\"0.5\" value=\"".$default_cn_greater_than."\" oninput=\"document.querySelector('#cngreaterthanvalue').value = value;\">";
echo "<output for=\"cngreaterthan\" id=\"cngreaterthanvalue\">".$default_cn_greater_than."</output>";
echo "<p style=\"font-size:75%; line-height: normal;\">Return amplified variants with a copy number above this value. <strong>To return all amplified variants, set this value to 2.</strong> All variants with no copy number will be returned.</p>";
echo "<p class=\"query_label\">Return amplified variants with a copy number above this value. <strong>To return all amplified variants, set this value to 2.</strong> All variants with no copy number will be returned.</p>";
echo "</section>";
echo "</div>";
@@ -97,7 +97,7 @@
$input_search_regions .= "placeholder=\"e.g. chr2:15483-25583;chr1:37211-67824;chr5;MT\">";
}
echo $input_search_regions; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple regions to search with a <strong>semicolon</strong>. To search all regions, leave this box blank. Any genes specified will be restricted to these coordinates.</p>";
echo "<p class=\"query_label\">Separate multiple regions to search with a <strong>semicolon</strong>. To search all regions, leave this box blank. Any genes specified will be restricted to these coordinates.</p>";
######################
@@ -133,7 +133,7 @@
$input_search_genes .= "placeholder=\"e.g. BRCA1;PIK3CA;TP53\">";
}
echo $input_search_genes; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple genes with a semicolon, comma or space. To search all genes, leave this box blank.</p>";
echo "<p class=\"query_label\">Separate multiple genes with a semicolon, comma or space. To search all genes, leave this box blank.</p>";
echo "</section>";
@@ -154,7 +154,7 @@
$input_exclude_regions .= "placeholder=\"e.g. chr2:15483-25583;chr1:37211-67824;chr5;MT\">";
}
echo $input_exclude_regions; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple regions to exclude with a <strong>semicolon</strong>. To search all regions, leave this box blank. Any genes specified will be restricted to these coordinates.</p>";
echo "<p class=\"query_label\">Separate multiple regions to exclude with a <strong>semicolon</strong>. To search all regions, leave this box blank. Any genes specified will be restricted to these coordinates.</p>";
######################
@@ -190,7 +190,7 @@
$input_exclude_genes .= "placeholder=\"e.g. BRCA1;PIK3CA;TP53\">";
}
echo $input_exclude_genes; # Print the box
echo "<p style=\"font-size:75%;\">Separate multiple genes with a semicolon, comma or space. To not exclude any genes, leave this box blank.</p>";
echo "<p class=\"query_label\">Separate multiple genes with a semicolon, comma or space. To not exclude any genes, leave this box blank.</p>";
echo "</section>";
@@ -290,7 +290,7 @@
echo "<input type=\"range\" name=\"min_cadd\" id=\"min_cadd\" min=\"0\" max=\"30\" step=\"1\" value=\"".$default_scaled_cadd_score."\" oninput=\"outputUpdateMinCADD(value)\">";
echo "<output for=\"min_cadd\" id=\"mincaddvalue\">".$default_scaled_cadd_score."</output><br />";
echo "<p style=\"font-size:75%;\"><strong>All variants without CADD scores are returned.</strong> For no minimum scaled CADD score, set this value to 0.</p>";
echo "<p class=\"query_label\"><strong>All variants without CADD scores are returned.</strong> For no minimum scaled CADD score, set this value to 0.</p>";
echo "<script>"; # Function for updating the real-time slider values
echo "function outputUpdateMinCADD(val) {";
@@ -352,7 +352,7 @@
echo "<input type=\"range\" name=\"exacmaf\" id=\"exacmaf\" min=\"0\" max=\"10\" step=\"0.1\" value=\"".$default_exac_frequency."\" oninput=\"document.querySelector('#exacmafvalue').value = value;\">";
echo "<output for=\"exacmaf\" id=\"exacmafvalue\">".$default_exac_frequency."</output>%";
echo "<p style=\"font-size:75%;\">Variants will be returned that are either below the allele frequency set or not present in the database. <strong>For no minimum allele frequency, set the value to 0%.</strong></p>";
echo "<p class=\"query_label\">Variants will be returned that are either below the allele frequency set or not present in the database. <strong>For no minimum allele frequency, set the value to 0%.</strong></p>";
// Custom dbsnp columns
if ($_SESSION["dbsnp_columns_exist"] == 1) {
@@ -400,7 +400,7 @@
echo "<input type=\"range\" name=\"min_seq_depth\" id=\"min_seq_depth\" min=\"0\" max=\"100\" step=\"10\" value=\"".$default_sequencing_depth."\" oninput=\"outputUpdateNumSeqDepth(value)\">";
echo "<output for=\"min_seq_depth\" id=\"numminseqdepthvalue\">".$default_sequencing_depth."</output><br />";
echo "<p style=\"font-size:75%;\">For no minimum sequencing depth, set this value to 0.</p>";
echo "<p class=\"query_label\">For no minimum sequencing depth, set this value to 0.</p>";
echo "<script>"; # Function for updating the real-time slider values
echo "function outputUpdateNumSeqDepth(val) {";
@@ -425,7 +425,7 @@
echo "<input type=\"range\" name=\"min_qual\" id=\"min_qual\" min=\"0\" max=\"1000\" step=\"20\" value=\"".$default_minimum_variant_quality."\" oninput=\"outputUpdateMinQual(value)\">";
echo "<output for=\"min_qual\" id=\"minqualvalue\">".$default_minimum_variant_quality."</output><br />";
echo "<p style=\"font-size:75%;\">For no minimum variant quality, set this value to 0.</p>";
echo "<p class=\"query_label\">For no minimum variant quality, set this value to 0.</p>";
echo "<script>"; # Function for updating the real-time slider values
echo "function outputUpdateMinQual(val) {";

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