Mercurial > repos > peterjc > fastq_paired_unpaired

changeset 8:8cbc866b72ce draft

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"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:36:15 +0000
parents 2709a0f065c9
children 422724644e24
files tools/fastq_paired_unpaired/README.rst tools/fastq_paired_unpaired/fastq_paired_unpaired.py tools/fastq_paired_unpaired/fastq_paired_unpaired.xml tools/fastq_paired_unpaired/tool_dependencies.xml
diffstat 4 files changed, 39 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/tools/fastq_paired_unpaired/README.rst	Tue May 16 08:53:57 2017 -0400
+++ b/tools/fastq_paired_unpaired/README.rst	Fri Apr 16 22:36:15 2021 +0000
@@ -105,7 +105,7 @@
 
     $ planemo shed_upload --tar_only tools/fastq_paired_unpaired/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/sanger-pairs-forward.fastq
     test-data/sanger-pairs-interleaved.fastq
     test-data/sanger-pairs-mixed.fastq
--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.py	Tue May 16 08:53:57 2017 -0400
+++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.py	Fri Apr 16 22:36:15 2021 +0000
@@ -4,7 +4,7 @@
 The input file should be a valid FASTQ file which has been sorted so that
 any partner forward+reverse reads are consecutive. The output files all
 preserve this sort order. Pairing are recognised based on standard name
-suffices. See below or run the tool with no arguments for more details.
+suffixes. See below or run the tool with no arguments for more details.
 
 Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
 Color Space should all work equally well).
@@ -122,8 +122,12 @@
 re_illumina_r = re.compile(r"^[a-zA-Z0-9_:-]+ 2:.*$")
 assert re_illumina_f.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA")
 assert re_illumina_r.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA")
-assert not re_illumina_f.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA")
-assert not re_illumina_r.match("HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA")
+assert not re_illumina_f.match(
+    "HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA"
+)
+assert not re_illumina_r.match(
+    "HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA"
+)
 
 FASTQ_TEMPLATE = "@%s\n%s\n+\n%s\n"
 
@@ -147,7 +151,7 @@
         # ============
         # Forward read
         # ============
-        template = name[:suffix.start()]
+        template = name[: suffix.start()]
         is_forward = True
     elif re_illumina_f.match(title):
         template = name  # No suffix
@@ -172,7 +176,7 @@
             # ============
             # Reverse read
             # ============
-            template = name[:suffix.start()]
+            template = name[: suffix.start()]
             is_reverse = True
         elif re_illumina_r.match(title):
             template = name  # No suffix
@@ -226,12 +230,25 @@
     pairs_r_handle.close()
 
 if neither:
-    print("%i reads (%i forward, %i reverse, %i neither), %i in pairs, %i as singles"
-          % (count, forward, reverse, neither, pairs, singles))
+    print(
+        "%i reads (%i forward, %i reverse, %i neither), %i in pairs, %i as singles"
+        % (count, forward, reverse, neither, pairs, singles)
+    )
 else:
-    print("%i reads (%i forward, %i reverse), %i in pairs, %i as singles"
-          % (count, forward, reverse, pairs, singles))
+    print(
+        "%i reads (%i forward, %i reverse), %i in pairs, %i as singles"
+        % (count, forward, reverse, pairs, singles)
+    )
 
-assert count == pairs + singles == forward + reverse + neither, \
-    "%i vs %i+%i=%i vs %i+%i+%i=%i" \
-    % (count, pairs, singles, pairs + singles, forward, reverse, neither, forward + reverse + neither)
+assert (
+    count == pairs + singles == forward + reverse + neither
+), "%i vs %i+%i=%i vs %i+%i+%i=%i" % (
+    count,
+    pairs,
+    singles,
+    pairs + singles,
+    forward,
+    reverse,
+    neither,
+    forward + reverse + neither,
+)
--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml	Tue May 16 08:53:57 2017 -0400
+++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml	Fri Apr 16 22:36:15 2021 +0000
@@ -1,5 +1,5 @@
 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4">
-    <description>using the read name suffices</description>
+    <description>using the read name suffixes</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
@@ -17,7 +17,7 @@
 $output_singles
     </command>
     <inputs>
-        <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
+        <param name="input_fastq" type="data" format="foobar" label="FASTQ file to divide into paired and unpaired reads"/>
         <conditional name="output_choice_cond">
             <param name="output_choice" type="select" label="How to output paired reads?">
                 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
@@ -65,7 +65,7 @@
 The input file should be a valid FASTQ file which has been sorted so that
 any partner forward+reverse reads are consecutive. The output files all
 preserve this sort order. Pairing are recognised based on standard name
-suffices. See below or run the tool with no arguments for more details.
+suffixes. See below or run the tool with no arguments for more details.
 
 Any reads where the forward/reverse naming suffix used is not recognised
 are treated as orphan reads. The tool supports the /1 and /2 convention
@@ -75,7 +75,7 @@
 with the fragment number in the description, for example:
 
  * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
- * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA 
+ * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
 
 Note that this does support multiple forward and reverse reads per template
 (which is quite common with Sanger sequencing), e.g. this which is sorted
@@ -106,7 +106,7 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
--- a/tools/fastq_paired_unpaired/tool_dependencies.xml	Tue May 16 08:53:57 2017 -0400
+++ b/tools/fastq_paired_unpaired/tool_dependencies.xml	Fri Apr 16 22:36:15 2021 +0000
@@ -1,9 +1,9 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="galaxy_sequence_utils" version="1.0.1">
-        <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="c1ab450748ba"/>
     </package>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="a12f73c3b116"/>
     </package>
-</tool_dependency>
+</tool_dependency>
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