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comparison crossmap.xml @ 7:1efce8a693ca draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
author yhoogstrate
date Thu, 12 Nov 2015 16:08:56 -0500
parents 5ef4ac8f2956
children
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6:5ef4ac8f2956 7:1efce8a693ca
12 <regex match=".*" source="both" level="log"/> 12 <regex match=".*" source="both" level="log"/>
13 </stdio> 13 </stdio>
14 14
15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> 15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
16 16
17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> 17 <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
18 <command><![CDATA[
18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 19 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
19 ${multiple.input_format.replace("sam","bam")} 20 ${multiple.input_format.replace("sam","bam")}
20 21
21 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached" 22 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> 23 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
42 #end if 43 #end if
43 44
44 "$output" 45 "$output"
45 46
46 #if $multiple.input_format in ["bam", "sam"] 47 #if $multiple.input_format in ["bam", "sam"]
47 ; mv "${output}.${multiple.input_format}" "$output" 48 && mv "${output}.${multiple.input_format}" "$output"
48 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped" 49 && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
49 #else if $multiple.input_format in ["vcf"] 50 #else if $multiple.input_format in ["vcf"]
50 ; mv "${output}" "$output" 51 && mv "${output}" "$output"
51 ; mv "${output}.unmap" "$output_unmapped" 52 && mv "${output}.unmap" "$output_unmapped"
52 #else if $multiple.input_format in ["wig", "bigwig"] 53 #else if $multiple.input_format in ["wig", "bigwig"]
53 ; mv "${output}.bw" "$output" 54 && mv "${output}.bw" "$output"
54 ; mv "${output}.sorted.bgr" "$output2" 55 && mv "${output}.sorted.bgr" "$output2"
55 #end if 56 #end if
56 </command> 57 ]]></command>
57 58
58 <inputs> 59 <inputs>
59 <conditional name="multiple"> 60 <conditional name="multiple">
60 <param name="input_format" type="select" label="Convert a file of the following format"> 61 <param name="input_format" type="select" label="Convert a file of the following format">
61 <option value="bam">BAM</option> 62 <option value="bam">BAM</option>
71 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> 72 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
72 <option value="cached">Local data (in galaxy)</option> 73 <option value="cached">Local data (in galaxy)</option>
73 <option value="history">From History</option> 74 <option value="history">From History</option>
74 </param> 75 </param>
75 <when value="cached"> 76 <when value="cached">
76 <param type="data" format="bam" name="input" label="BAM/SAM file"> 77 <param type="data" format="bam" name="input" label="BAM file">
77 <validator type="unspecified_build" /> 78 <validator type="unspecified_build" />
78 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> 79 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
79 </param> 80 </param>
80 <param name="input_chain" type="select" label="Lift Over To"> 81 <param name="input_chain" type="select" label="Lift Over To">
81 <options from_file="liftOver.loc"> 82 <options from_file="liftOver.loc">
103 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> 104 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
104 <option value="cached">Local data (in galaxy)</option> 105 <option value="cached">Local data (in galaxy)</option>
105 <option value="history">From History</option> 106 <option value="history">From History</option>
106 </param> 107 </param>
107 <when value="cached"> 108 <when value="cached">
108 <param type="data" format="sam" name="input" label="BAM/SAM file"> 109 <param type="data" format="sam" name="input" label="SAM file">
109 <validator type="unspecified_build" /> 110 <validator type="unspecified_build" />
110 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> 111 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
111 </param> 112 </param>
112 <param name="input_chain" type="select" label="Lift Over To"> 113 <param name="input_chain" type="select" label="Lift Over To">
113 <options from_file="liftOver.loc"> 114 <options from_file="liftOver.loc">
332 </outputs> 333 </outputs>
333 334
334 <tests> 335 <tests>
335 <!-- BAM/SAM --> 336 <!-- BAM/SAM -->
336 <test> 337 <test>
338 <param name="input_format" value="bam"/>
339 <param name="index_source" value="history"/>
340 <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/>
341 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
342 <param name="include_fails" value="False"/>
343
344 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
345 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
346 </test>
347
348 <test>
337 <param name="input_format" value="sam"/> 349 <param name="input_format" value="sam"/>
338 <param name="index_source" value="history"/> 350 <param name="index_source" value="history"/>
339 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/> 351 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
340 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 352 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
341 <param name="include_fails" value="False"/> 353 <param name="include_fails" value="False"/>