changeset 0:6d5d1b56c286 draft

Uploaded
author jackcurragh
date Wed, 23 Mar 2022 12:53:08 +0000
parents
children 27f3669eda60
files get_chrom_sizes/get_chrom_sizes.xml get_chrom_sizes/test-data/test.fasta.fai get_chrom_sizes/test-data/test.fasta.sizes
diffstat 3 files changed, 13408 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Wed Mar 23 12:53:08 2022 +0000
@@ -0,0 +1,24 @@
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="1.0">
+    <description>order of storing aligned sequences</description>
+    <command><![CDATA[
+        cut -f1,2 '${input1}' > '${output1}' 
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="fai" label="FASTA FAI File" />
+    </inputs>
+    <outputs>
+       <data name="output1" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test.fasta.fai" ftype="fai" />
+            <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+creates a chromosome sizes file from a fai index
+    </help>
+    <citations/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_chrom_sizes/test-data/test.fasta.fai	Wed Mar 23 12:53:08 2022 +0000
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+YMR024W	1773	12723965	50	51
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+YMR046W_A	729	12773368	50	51
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+YMR059W	987	12806329	50	51
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+YMR300C	2133	13326560	50	51
+YMR301C	2673	13328745	50	51
+YMR302C	3153	13331481	50	51
+YMR303C	1647	13334707	50	51
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+YMR304C_A	951	13340786	50	51
+YMR305C	1770	13341766	50	51
+YMR306W	5958	13343581	50	51
+YMR306C_A	990	13349670	50	51
+YMR307W	2280	13350689	50	51
+YMR307C_A	795	13353026	50	51
+YMR308C	3870	13353846	50	51
+YMR309C	3039	13357803	50	51
+YMR310C	1554	13360912	50	51
+YMR311C	1290	13362507	50	51
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+YMR314W	1305	13367881	50	51
+YMR315W	1650	13369222	50	51
+YMR315W_A	708	13370916	50	51
+YMR316W	1611	13371648	50	51
+YMR316C_A	912	13373303	50	51
+YMR316C_B	909	13374245	50	51
+YMR317W	4023	13375182	50	51
+YMR318C	1683	13379295	50	51
+YMR319C	2259	13381021	50	51
+YMR320W	906	13383335	50	51
+YMR321C	918	13384269	50	51
+YMR322C	1314	13385215	50	51
+YMR323W	1914	13386565	50	51
+YMR324C	843	13388527	50	51
+YMR325W	975	13389396	50	51
+YMR326C	909	13390400	50	51
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_chrom_sizes/test-data/test.fasta.sizes	Wed Mar 23 12:53:08 2022 +0000
@@ -0,0 +1,6692 @@
+YAL012W	1785
+YAL069W	915
+YAL068W_A	855
+YAL068C	963
+YAL067W_A	828
+YAL067C	2382
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+YAL064W_B	981
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+YAL063C_A	891
+YAL063C	4569
+YAL062W	1974
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