Mercurial > repos > devteam > fastx_renamer

changeset 2:2b324adf4e58 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:52:31 -0400
parents defaa5ba1ee2
children d8baeed2ce62
files fastx_renamer.xml macros.xml test-data/fastx_renamer-in1.fastq test-data/fastx_renamer-out1.fastq test-data/input.fastqsolexa test-data/renamed_nt_sequence.fastqsolexa tool_dependencies.xml
diffstat 7 files changed, 156 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/fastx_renamer.xml	Tue Oct 13 12:41:46 2015 -0400
+++ b/fastx_renamer.xml	Tue May 08 12:52:31 2018 -0400
@@ -1,19 +1,19 @@
-<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
+<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
-#if $input.ext == "fastqsanger":
-    -Q 33
-#end if
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_renamer
+-n $TYPE
+-o '$output'
+-v
+@FQQUAL@
+    ]]></command>
 
     <inputs>
-        <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
+        <expand macro="fastx_input" />
 
         <param name="TYPE" type="select" label="Rename sequence identifiers to">
             <option value="SEQ">Nucleotides sequence</option>
@@ -22,11 +22,16 @@
     </inputs>
 
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="fastx_renamer-in1.fastq" />
+            <param name="TYPE" value="SEQ" />
+            <output name="output" file="fastx_renamer-out1.fastq" />
+        </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool renames the sequence identifiers in a FASTQ/A file.
@@ -65,6 +70,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
-<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+    ]]></help>
+    <expand macro="citations" />
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 08 12:52:31 2018 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@CATS@">
+        #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+            zcat -f '$input' |
+        #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+            bzcat -f '$input' |
+        #else:
+            cat '$input' |
+        #end if
+    </token>
+    <token name="@FQQUAL@">
+        <![CDATA[
+            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
+                -Q 33
+            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
+                -Q 64
+            #end if
+        ]]>
+    </token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@VERSION@">0.0.14</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>
+    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
+    <token name="@FASTAS@">fasta,fasta.gz</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{agordon,
+                    author = "Assaf Gordon",
+                    title = "FASTQ/A short-reads pre-processing tools",
+                    year = "2010",
+                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
+                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
+            </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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_renamer-in1.fastq	Tue May 08 12:52:31 2018 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_renamer-out1.fastq	Tue May 08 12:52:31 2018 -0400
@@ -0,0 +1,36 @@
+@GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@AATTATTTATTAAATTTTAATAATATGGGAGACACT
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++AATTATTTATTAAATTTTAATAATATGGGAGACACT
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@AATTCAAACCACCCCAACCCACACACAGAGATACAA
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++AATTCAAACCACCCCAACCCACACACAGAGATACAA
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fastqsolexa	Tue May 08 12:52:31 2018 -0400
@@ -0,0 +1,4 @@
+@CSHL_4_FC042GAMMII_2_1_517_596
+GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
++CSHL_4_FC042GAMMII_2_1_517_596
+40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/renamed_nt_sequence.fastqsolexa	Tue May 08 12:52:31 2018 -0400
@@ -0,0 +1,4 @@
+@GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
++GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
--- a/tool_dependencies.xml	Tue Oct 13 12:41:46 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>