Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 58:4c6df851e262 draft default tip
"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(-) [+] |
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--- 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, İnanç +"Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, İnanç 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> </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> </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