Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 58:4c6df851e262 draft default tip

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"planemo upload commit 1a7731bb4fe2e80fb1fdc88121783068af3edb08"
author rhpvorderman
date Fri, 21 Apr 2023 10:04:39 +0000
parents 33412e85e669
children
files CHANGES.md complete_immunerepertoire.xml convert_windows_to_utf-8.py report_clonality/naive_cdr3_char.htm report_clonality/naive_circos.htm report_clonality/naive_clonality.htm report_clonality/naive_compare.htm report_clonality/naive_downloads.htm report_clonality/naive_gene_freq.htm report_clonality/naive_heatmap.htm report_clonality/naive_junction.htm report_clonality/naive_overview.htm report_clonality/r_wrapper.sh
diffstat 13 files changed, 48 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/CHANGES.md	Wed Feb 02 10:50:01 2022 +0000
+++ b/CHANGES.md	Fri Apr 21 10:04:39 2023 +0000
@@ -1,3 +1,8 @@
+version 1.1.1
+-------------
++ Make sure the path to the zip is correct.
++ The html files are now UTF-8 encoded to prevent decoding errors.
+
 version 1.1.0
 -------------
 + Add a container requirement to allow using docker or singularity.
--- a/complete_immunerepertoire.xml	Wed Feb 02 10:50:01 2022 +0000
+++ b/complete_immunerepertoire.xml	Fri Apr 21 10:04:39 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.0">
+<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.1">
 	<requirements>
         <requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="3.0.0">r-ggplot2</requirement>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_windows_to_utf-8.py	Fri Apr 21 10:04:39 2023 +0000
@@ -0,0 +1,14 @@
+import argparse
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("files", nargs="+")
+    args = parser.parse_args()
+    for file in args.files:
+        with open(file, "rb") as in_r:
+            data = in_r.read()
+        text = data.decode("windows-1252")
+        text = text.replace("charset=windows-1252", "charset=\"UTF-8\"", 1)
+        with open(file, "wt", encoding="UTF-8") as out:
+            out.write(text)
+
--- a/report_clonality/naive_cdr3_char.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_cdr3_char.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
--- a/report_clonality/naive_circos.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_circos.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
@@ -43,7 +43,7 @@
 <div class=WordSection1>
 
 <p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
-"Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, &#304;nanç
+"Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, &#304;nanç
 Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco
 A. Marra (2009). Circos: An information aesthetic for comparative genomics. In <i>Genome
 Research 10.1101/gr.092759.109</i>.</span></p>
--- a/report_clonality/naive_clonality.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_clonality.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
@@ -46,8 +46,8 @@
 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>For each donor a
 subtab is provided containing information on the sequence overlap between
 replicates of the different replicates of one donor. Dependent on the settings
-of the Shared clonal types / clonality filter a clonality score is given.  The clonality
-score  is calculated according to the formula described by </span><a
+of the Shared clonal types / clonality filter a clonality score is given.  The clonality
+score  is calculated according to the formula described by </span><a
 name="OLE_LINK13"></a><a name="OLE_LINK12"></a><a name="OLE_LINK11"><span
 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Boyd
 et al, PMID: 20161664. </span></a></p>
--- a/report_clonality/naive_compare.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_compare.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
--- a/report_clonality/naive_downloads.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_downloads.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
@@ -66,7 +66,7 @@
 
 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'>The dataset used to generate  the
+font-family:"Times New Roman","serif"'>The dataset used to generate  the
 distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
 font-family:"Times New Roman","serif"'>Downloads a table with information used
 to generate the distribution of D gene families graph.</span></p>
@@ -126,21 +126,21 @@
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VD heatmap for “donor name”:</span></u><span
+data used to generate the VD heatmap for “donor name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the VD heatmap. For each
 uploaded donor a separate download is generated.</span></p>
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VJ heatmap for “donor name”:</span></u><span
+data used to generate the VJ heatmap for “donor name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the VJ heatmap. For each
 uploaded donor a separate download is generated.</span></p>
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the DJ heatmap for “sample name”:</span></u><span
+data used to generate the DJ heatmap for “sample name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the DJ heatmap. For each
 uploaded donor a separate download is generated.</span></p>
@@ -150,21 +150,21 @@
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VD circus plots for “donor name”:</span></u><span
+data used to generate the VD circus plots for “donor name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the VD heatmap. For each
 uploaded donor a separate download is generated.</span></p>
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VJ circus plots for “donor name”:</span></u><span
+data used to generate the VJ circus plots for “donor name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the VJ heatmap. For each
 uploaded donor a separate download is generated.</span></p>
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the DJ circus plots for “sample name”:</span></u><span
+data used to generate the DJ circus plots for “sample name”:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the DJ heatmap. For each
 uploaded donor a separate download is generated.</span></p>
--- a/report_clonality/naive_gene_freq.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_gene_freq.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,11 +1,7 @@
-<html xmlns:v="urn:schemas-microsoft-com:vml"
-xmlns:o="urn:schemas-microsoft-com:office:office"
-xmlns:w="urn:schemas-microsoft-com:office:word"
-xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
-xmlns="http://www.w3.org/TR/REC-html40">
+<html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=ProgId content=Word.Document>
 <meta name=Generator content="Microsoft Word 14">
 <meta name=Originator content="Microsoft Word 14">
@@ -169,8 +165,8 @@
 OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";
 mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all
 uploaded donors. The order of the V genes on the x-axis can be altered by
-altering the “<span style='color:black;background:white'>Order of V(D)J genes
-in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span
+altering the “<span style='color:black;background:white'>Order of V(D)J genes
+in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span
 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";
 color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p>
 
@@ -184,8 +180,8 @@
 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
 style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
 EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The
-order of the D genes on the x-axis can be altered by altering the “<span
-style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
+order of the D genes on the x-axis can be altered by altering the “<span
+style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
 the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p>
 
 <p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
@@ -198,8 +194,8 @@
 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
 style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
 EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The
-order of the J genes on the x-axis can be altered by altering the “<span
-style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
+order of the J genes on the x-axis can be altered by altering the “<span
+style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
 the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p>
 
 <p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
--- a/report_clonality/naive_heatmap.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_heatmap.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
--- a/report_clonality/naive_junction.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_junction.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,11 +1,7 @@
-<html xmlns:v="urn:schemas-microsoft-com:vml"
-xmlns:o="urn:schemas-microsoft-com:office:office"
-xmlns:w="urn:schemas-microsoft-com:office:word"
-xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
-xmlns="http://www.w3.org/TR/REC-html40">
+<html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=ProgId content=Word.Document>
 <meta name=Generator content="Microsoft Word 14">
 <meta name=Originator content="Microsoft Word 14">
--- a/report_clonality/naive_overview.htm	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/naive_overview.htm	Fri Apr 21 10:04:39 2023 +0000
@@ -1,7 +1,7 @@
 <html>
 
 <head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
 <meta name=Generator content="Microsoft Word 14 (filtered)">
 <style>
 <!--
--- a/report_clonality/r_wrapper.sh	Wed Feb 02 10:50:01 2022 +0000
+++ b/report_clonality/r_wrapper.sh	Fri Apr 21 10:04:39 2023 +0000
@@ -365,7 +365,7 @@
 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
-echo "<tr><td>All outputs below in a zip file</td><td><a href='$ALL_OUTPUTS_ZIP'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>All outputs below in a zip file</td><td><a href='all_outputs.zip'>Download</a></td></tr>" >> $outputFile
 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile