Mercurial > repos > jdv > nanopore_qc

changeset 5:f2081dc93880 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 1dee763b48c54e1c538f75b7f0de2f5a0ed25d4d
author jdv
date Mon, 12 Mar 2018 19:55:54 -0400
parents 4b7d1bcf210c
children 0cf41189f086
files nanopore_qc.xml test-data/output.html.small.q10 test-data/output.html.small.q6
diffstat 3 files changed, 23 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/nanopore_qc.xml	Mon Mar 12 15:04:45 2018 -0400
+++ b/nanopore_qc.xml	Mon Mar 12 19:55:54 2018 -0400
@@ -3,18 +3,18 @@
     <description>Quality report for nanopore data</description>
 
     <requirements>
-        <requirement type="package" version="3.3.1">r-base</requirement>
-        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
-        <requirement type="package" version="1.8.4">r-plyr</requirement>
-        <requirement type="package" version="1.4.2">r-reshape2</requirement>
-        <requirement type="package" version="0.2.2">r-readr</requirement>
-        <requirement type="package" version="2.1.14">r-yaml</requirement>
-        <requirement type="package" version="0.4.1">r-scales</requirement>
-        <requirement type="package" version="1.4.1">r-futile.logger</requirement>
-        <requirement type="package" version="1.10.4">r-data.table</requirement>
-        <requirement type="package" version="1.3.2">r-optparse</requirement>
-        <requirement type="package" version="1.8">r-mgcv</requirement>
-        <requirement type="package" version="0.66">perl-yaml-libyaml</requirement>
+        <requirement type="package" version=">=3.3.1">r-base</requirement>
+        <requirement type="package" version=">=2.2.1">r-ggplot2</requirement>
+        <requirement type="package" version=">=1.8.4">r-plyr</requirement>
+        <requirement type="package" version=">=1.4.2">r-reshape2</requirement>
+        <requirement type="package" version=">=0.2.2">r-readr</requirement>
+        <requirement type="package" version=">=2.1.14">r-yaml</requirement>
+        <requirement type="package" version=">=0.4.1">r-scales</requirement>
+        <requirement type="package" version=">=1.4.1">r-futile.logger</requirement>
+        <requirement type="package" version=">=1.10.4">r-data.table</requirement>
+        <requirement type="package" version=">=1.3.2">r-optparse</requirement>
+        <requirement type="package" version=">=1.8">r-mgcv</requirement>
+        <requirement type="package" version=">=0.66">perl-yaml-libyaml</requirement>
     </requirements>
 
     <stdio>
@@ -71,12 +71,14 @@
     </tests>
     <help>
 <![CDATA[
+    `NanoporeQC` produces a QC report for nanopore sequencing data. It utilizes
+    the summary table produced by Albacore, which saves time by avoiding the
+    need to re-parse the FAST5 read data. `NanoporeQC` was originally forked
+    from the `minion_qc` codebase (https://github.com/roblanf/minion_qc).
 
-    `NanoporeQC` produces a summary report on nanopore read data called by
-    Albacore. It acts on the summary table produced by Albacore and produces
-    HTML output. It was originally forked from the MinionQC code by Robert
-    Lanfear.
-
+    The only tuneable parameter is the quality value cutoff. Two summaries are
+    produced for each table and plot -- one for all reads (with length >= 0)
+    and one for reads with a quality value greater than the cutoff.
 ]]>
     </help>
     <citations>
--- a/test-data/output.html.small.q10	Mon Mar 12 15:04:45 2018 -0400
+++ b/test-data/output.html.small.q10	Mon Mar 12 19:55:54 2018 -0400
@@ -76,11 +76,11 @@
         </tr>
         <tr>
             <td>Total Reads</td>
-            <td>9999</td>
+            <td>9990</td>
         </tr>
         <tr>
             <td>Mean Length</td>
-            <td>927.8</td>
+            <td>928.7</td>
         </tr>
         <tr>
             <td>Median Length</td>
--- a/test-data/output.html.small.q6	Mon Mar 12 15:04:45 2018 -0400
+++ b/test-data/output.html.small.q6	Mon Mar 12 19:55:54 2018 -0400
@@ -76,11 +76,11 @@
         </tr>
         <tr>
             <td>Total Reads</td>
-            <td>9999</td>
+            <td>9990</td>
         </tr>
         <tr>
             <td>Mean Length</td>
-            <td>927.8</td>
+            <td>928.7</td>
         </tr>
         <tr>
             <td>Median Length</td>