Mercurial > repos > bebatut > extract_min_max_lines

changeset 1:07c9ae09ae38 draft default tip

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/extract_min_max_lines commit 718c006213709b631862b8d6d655fafc92e79ef7-dirty
author bebatut
date Fri, 15 Apr 2016 07:58:25 -0400
parents 42e4aee6b1fa
children
files extract_min_max_lines.xml test-data/output_file.txt test-data/output_test_col_3_max.tabular test-data/output_test_col_3_min.tabular test-data/output_test_col_4_max.tabular test-data/output_test_col_4_min.tabular
diffstat 6 files changed, 72 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/extract_min_max_lines.xml	Tue Apr 12 02:58:49 2016 -0400
+++ b/extract_min_max_lines.xml	Fri Apr 15 07:58:25 2016 -0400
@@ -1,5 +1,5 @@
 <tool id="extract_min_max_lines" name="Extract lines corresponding" version="0.1.0">
-    <description>with minimum and maximum values of a column</description>
+    <description>to minimum and maximum values of a column</description>
 
     <requirements>
     </requirements>
@@ -37,13 +37,42 @@
     </outputs>
 
     <tests>
+        <test>
+            <param name="input_file" value="input_file.tabular"/>
+            <param name="column_id" value="3"/>
+            <param name="extraction_type" value="min"/>
+            <param name="extraction_nb" value="10"/>
+            <output name="output_file" file="output_test_col_3_min.tabular"/>
+        </test>
+        <test>
+            <param name="input_file" value="input_file.tabular"/>
+            <param name="column_id" value="3"/>
+            <param name="extraction_type" value="max"/>
+            <param name="extraction_nb" value="10"/>
+            <output name="output_file" file="output_test_col_3_max.tabular"/>
+        </test>
+        <test>
+            <param name="input_file" value="input_file.tabular"/>
+            <param name="column_id" value="4"/>
+            <param name="extraction_type" value="min"/>
+            <param name="extraction_nb" value="10"/>
+            <output name="output_file" file="output_test_col_4_min.tabular"/>
+        </test>
+        <test>
+            <param name="input_file" value="input_file.tabular"/>
+            <param name="column_id" value="4"/>
+            <param name="extraction_type" value="max"/>
+            <param name="extraction_nb" value="10"/>
+            <output name="output_file" file="output_test_col_4_max.tabular"/>
+        </test>
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**What it does**
 
-        This tool extract lines from a tabular file corresponding to minimum or maximum values of a column.
+This tool extract a variable number of lines corresponding to minimum or maximum values of a chosen column.
 
+The file must be in tabular format with tabular separated columns. To chosen column to extract minimum or maximum values must be data columns.
     ]]></help>
 
     <citations>
--- a/test-data/output_file.txt	Tue Apr 12 02:58:49 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-UniRef50_P19529	Replication initiation protein	0.961640316151	0.326879196825	-0.634761119326
-UniRef50_Q5HJZ6	Plasmid recombination enzyme type 3	0.740800531361	0.244512495215	-0.496288036146
-UniRef50_P02983	Tetracycline resistance protein	0.573449640169	0.199788693154	-0.373660947015
-UniRef50_Q93GF3	Rep	0.410004761703	0.131513750747	-0.278491010956
-UniRef50_V6QG63	Integrase	0.340495265028	0.114492453346	-0.226002811682
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test_col_3_max.tabular	Fri Apr 15 07:58:25 2016 -0400
@@ -0,0 +1,10 @@
+UniRef50_P19529	Replication initiation protein	0.961640316151	0.326879196825	-0.634761119326
+UniRef50_Q5HJZ6	Plasmid recombination enzyme type 3	0.740800531361	0.244512495215	-0.496288036146
+UniRef50_P02983	Tetracycline resistance protein	0.573449640169	0.199788693154	-0.373660947015
+UniRef50_Q93GF3	Rep	0.410004761703	0.131513750747	-0.278491010956
+UniRef50_V6QG63	Integrase	0.340495265028	0.114492453346	-0.226002811682
+UniRef50_W1W6K4		0.278232683798	0.0628932216423	-0.215339462156
+UniRef50_D4FM51	Plasmid recombination enzyme	0.240102320308	0.0660335100375	-0.17406881027
+UniRef50_Z6ILY0		0.226654902022	0.0411737778722	-0.18548112415
+UniRef50_F0P516	Replication initiation protein, truncated	0.219429720121	0.0852047566562	-0.134224963465
+UniRef50_Q8CU99		0.194123181874	0.0585038462355	-0.135619335638
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test_col_3_min.tabular	Fri Apr 15 07:58:25 2016 -0400
@@ -0,0 +1,10 @@
+UniRef50_D3E2A1	Adhesin like protein	9.04497122279e-08	2.28645810921e-07	1.38196098693e-07
+UniRef50_A0A011N6I9		1.51918001834e-07	4.01161738419e-07	2.49243736585e-07
+UniRef50_UPI0004446091	PREDICTED	1.55078193737e-07	2.42316800842e-07	8.7238607105e-08
+UniRef50_W7A2A5		1.56660464008e-07	3.52580982773e-07	1.95920518765e-07
+UniRef50_UPI000349BE1A	hypothetical protein	1.75130162644e-07	1.32946712678e-06	1.15433696414e-06
+UniRef50_UPI0001BF6B99	90S preribosome component RRP12	1.84742307319e-07	4.34052266133e-06	4.15578035401e-06
+UniRef50_UPI000443E2D6	PREDICTED	1.90475579618e-07	3.42990413301e-07	1.52514833683e-07
+UniRef50_R4LEH4	Yd repeat containing protein	1.97864528112e-07	3.11608997065e-07	1.13744468953e-07
+UniRef50_UPI000378A614	hypothetical protein	2.00347906511e-07	1.1435229597e-06	9.43175053189e-07
+UniRef50_X2D8N8	CCR4 NOT transcription complex subunit 1 like protein	2.073948527e-07	1.64110422442e-05	1.62036473915e-05
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test_col_4_max.tabular	Fri Apr 15 07:58:25 2016 -0400
@@ -0,0 +1,10 @@
+UniRef50_Q9R3J0	Transposase, putative	0.00225014042765	1.10930408506	1.10705394463
+UniRef50_F0RKJ6	Transposase IS4 family protein	0.00427372358825	0.871496431206	0.867222707618
+UniRef50_UPI0000164CF6	hypothetical protein DR_1761	0.000366361200249	0.367022323052	0.366655961852
+UniRef50_Q9RYQ5	Resolvase, putative	0.000674082122953	0.361753596131	0.361079514008
+UniRef50_P19529	Replication initiation protein	0.961640316151	0.326879196825	-0.634761119326
+UniRef50_F0RR64		0.000846315859607	0.301362181458	0.300515865598
+UniRef50_Q9RV33		0.000368878816464	0.284296397807	0.283927518991
+UniRef50_Q5HJZ6	Plasmid recombination enzyme type 3	0.740800531361	0.244512495215	-0.496288036146
+UniRef50_UPI0000164CD9	putative transposase	0.00104009031306	0.224490351769	0.223450261456
+UniRef50_Q9RYR2	Extracellular solute binding protein, family 5	0.00106094764695	0.224438113631	0.223377165984
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test_col_4_min.tabular	Fri Apr 15 07:58:25 2016 -0400
@@ -0,0 +1,10 @@
+UniRef50_F0YEL0		9.51325576245e-06	1.51416281297e-07	-9.36183948115e-06
+UniRef50_A0A058ZAA4		6.36876267111e-06	1.95527719833e-07	-6.17323495128e-06
+UniRef50_W4XFJ9		6.76030182537e-07	2.06555424425e-07	-4.69474758112e-07
+UniRef50_D3E2A1	Adhesin like protein	9.04497122279e-08	2.28645810921e-07	1.38196098693e-07
+UniRef50_UPI0004446091	PREDICTED	1.55078193737e-07	2.42316800842e-07	8.7238607105e-08
+UniRef50_UPI00036AFA97	hypothetical protein	1.94826634309e-05	2.65435474198e-07	-1.92172279567e-05
+UniRef50_UPI0003C3A0E4	PREDICTED	1.06134224488e-06	2.68380106598e-07	-7.92962138282e-07
+UniRef50_A0A024JLS1	Similar to Saccharomyces cerevisiae YLR106C MDN1 Huge dynein related AAA type ATPase 	1.04926977865e-06	2.78766826282e-07	-7.70502952368e-07
+UniRef50_UPI00031ABCD6	hypothetical protein	2.0828158654e-06	2.92321189728e-07	-1.79049467567e-06
+UniRef50_F0VBH0		1.74170711526e-05	3.07747069636e-07	-1.7109324083e-05