Mercurial > repos > devteam > fastq_to_fasta

changeset 6:77b41c89d856 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:53:23 +0000
parents 8979c288aefb
children
files fastq_to_fasta.xml macros.xml
diffstat 2 files changed, 19 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_to_fasta.xml	Tue Jun 27 17:37:28 2023 +0000
+++ b/fastq_to_fasta.xml	Thu Aug 10 06:53:23 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2">
+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>converter from FASTX-toolkit</description>
     <macros>
         <import>macros.xml</import>
--- a/macros.xml	Tue Jun 27 17:37:28 2023 +0000
+++ b/macros.xml	Thu Aug 10 06:53:23 2023 +0000
@@ -11,13 +11,22 @@
     </token>
     <token name="@FQQUAL@">
         <![CDATA[
-            #if 'fastqsanger' in $input.ext:
+            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
                 -Q 33
-            #elif 'fastqsolexa' in $input.ext or 'fastqillumina' in $input.ext:
+            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
                 -Q 64
             #end if
         ]]>
     </token>
+    <token name="@GZIP@">
+        <![CDATA[
+            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+                | gzip -c
+            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+                | bzip2 -c
+            #end if
+        ]]>
+    </token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
@@ -25,6 +34,7 @@
         </requirements>
     </xml>
     <token name="@VERSION@">0.0.14</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
     <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
     <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
@@ -42,7 +52,13 @@
             </citation>
         </citations>
     </xml>
+    <xml name="fasta_input">
+        <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
+    </xml>
     <xml name="fastq_input">
         <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
     </xml>
+    <xml name="fastx_input">
+        <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
+    </xml>
 </macros>