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changeset 0:ce0afe2b18d0 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
author dfornika
date Thu, 19 Sep 2019 19:57:29 -0400
parents
children ddae1e5b4bb2
files macros.xml micall-lite.xml test-data/1234A-V3LOOP_S1_L001_R1_001.fastq test-data/1234A-V3LOOP_S1_L001_R2_001.fastq
diffstat 4 files changed, 137 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Sep 19 19:57:29 2019 -0400
@@ -0,0 +1,9 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1rc2</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+            </citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/micall-lite.xml	Thu Sep 19 19:57:29 2019 -0400
@@ -0,0 +1,48 @@
+<tool id="micall-lite" name="micall-lite" version="@TOOL_VERSION@+galaxy0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
+    </requirements>
+    <version_command>micall --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+      micall
+        #if $single_paired.single_paired_selector == 'yes'
+            '${single_paired.forward_input}' '${single_paired.reverse_input}'
+        #elif $single_paired.single_paired_selector == "collection":
+            '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
+        #else:
+            '${single_paired.input_sequences}'
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="single_paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+                <option value="collection">Collection</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
+            </param>
+            <when value="collection">
+                <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
+            </when>
+            <when value="yes">
+                <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
+                <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
+            </when>
+            <when value="no">
+                <param format="fastq,fastq.gz" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP_S1_L001_R1_001.fastq	Thu Sep 19 19:57:29 2019 -0400
@@ -0,0 +1,40 @@
+@M01234:01:000000000-AAAAA:1:1101:01234:0001 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0002 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0003 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0004 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0005 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0006 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0007 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0008 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0009 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0010 1:N:0:1:fifth_base_differs
+TGTATAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP_S1_L001_R2_001.fastq	Thu Sep 19 19:57:29 2019 -0400
@@ -0,0 +1,40 @@
+@M01234:01:000000000-AAAAA:1:1101:01234:0001 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0002 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0003 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0004 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0005 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0006 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0007 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0008 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0009 2:N:0:1
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0010 2:N:0:1:fifth_base_differs
+CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTATACA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA