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https://github.com/galaxyproject/galaxy.git
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Add new functional tests for uploading composite data types lped and pbed - handles ticket # 173.
This commit is contained in:
Greg Von Kuster
@@ -162,9 +162,9 @@
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<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
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<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
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<!-- linkage format pedigree (separate .map file) -->
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<datatype extension="lped" type="galaxy.datatypes.genetics:Lped"/>
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<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"/>
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<!-- plink compressed file - has bed extension unfortunately -->
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<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed"/>
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<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"/>
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<!-- eigenstrat pedigree input file -->
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<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
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<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
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@@ -0,0 +1 @@
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l�����������������������οΎξΈ��όώΏ�ΏϋϊΏΏο/��ώ�ο―�κΈλκ°®Ύξ®γκΈ;μ/βοϊ―ο―ΞκΌοβ°―ώΟ�γ―ψ+μ?β�ϊ―ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ���ο�����Ί��ώ―ώοΏ�»��ώ���ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ�������ώο���ώ����ϋ�ϋ���»�ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ���ολ�κΎ�Ίϊοώ―ξλΏώ;―>βοώ»
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@@ -0,0 +1,10 @@
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22 rs5992809 16.5965 16596539 0 C
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||||
22 rs12168131 16.6573 16657262 G A
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||||
22 rs390041 16.6629 16662916 T C
|
||||
22 rs437633 16.6697 16669684 A G
|
||||
22 rs450960 16.6909 16690858 T C
|
||||
22 rs450975 16.6909 16690887 T C
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||||
22 rs451740 16.6912 16691174 T C
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||||
22 rs8139723 16.6917 16691696 T C
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22 rs405490 16.6922 16692175 G A
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22 rs415170 16.6935 16693517 G C
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@@ -0,0 +1,90 @@
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CH18526 NA18526 0 0 2 1
|
||||
CH18524 NA18524 0 0 1 1
|
||||
CH18529 NA18529 0 0 2 1
|
||||
CH18558 NA18558 0 0 1 1
|
||||
CH18532 NA18532 0 0 2 1
|
||||
CH18561 NA18561 0 0 1 1
|
||||
CH18562 NA18562 0 0 1 1
|
||||
CH18537 NA18537 0 0 2 2
|
||||
CH18603 NA18603 0 0 1 2
|
||||
CH18540 NA18540 0 0 2 1
|
||||
CH18605 NA18605 0 0 1 1
|
||||
CH18542 NA18542 0 0 2 1
|
||||
CH18545 NA18545 0 0 2 1
|
||||
CH18572 NA18572 0 0 1 2
|
||||
CH18547 NA18547 0 0 2 2
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CH18609 NA18609 0 0 1 1
|
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CH18550 NA18550 0 0 2 1
|
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CH18608 NA18608 0 0 1 1
|
||||
CH18552 NA18552 0 0 2 1
|
||||
CH18611 NA18611 0 0 1 1
|
||||
CH18555 NA18555 0 0 2 1
|
||||
CH18564 NA18564 0 0 2 2
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CH18566 NA18566 0 0 2 1
|
||||
CH18563 NA18563 0 0 1 1
|
||||
CH18570 NA18570 0 0 2 1
|
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CH18612 NA18612 0 0 1 2
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CH18571 NA18571 0 0 2 1
|
||||
CH18620 NA18620 0 0 1 1
|
||||
CH18621 NA18621 0 0 1 1
|
||||
CH18594 NA18594 0 0 2 1
|
||||
CH18622 NA18622 0 0 1 2
|
||||
CH18573 NA18573 0 0 2 2
|
||||
CH18623 NA18623 0 0 1 1
|
||||
CH18576 NA18576 0 0 2 1
|
||||
CH18577 NA18577 0 0 2 1
|
||||
CH18624 NA18624 0 0 1 1
|
||||
CH18579 NA18579 0 0 2 1
|
||||
CH18632 NA18632 0 0 1 2
|
||||
CH18582 NA18582 0 0 2 1
|
||||
CH18633 NA18633 0 0 1 1
|
||||
CH18635 NA18635 0 0 1 2
|
||||
CH18592 NA18592 0 0 2 1
|
||||
CH18636 NA18636 0 0 1 1
|
||||
CH18593 NA18593 0 0 2 2
|
||||
CH18637 NA18637 0 0 1 1
|
||||
JA18942 NA18942 0 0 2 2
|
||||
JA18940 NA18940 0 0 1 2
|
||||
JA18951 NA18951 0 0 2 2
|
||||
JA18943 NA18943 0 0 1 2
|
||||
JA18947 NA18947 0 0 2 2
|
||||
JA18944 NA18944 0 0 1 2
|
||||
JA18945 NA18945 0 0 1 2
|
||||
JA18949 NA18949 0 0 2 2
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JA18948 NA18948 0 0 1 2
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||||
JA18952 NA18952 0 0 1 2
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JA18956 NA18956 0 0 2 2
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JA18964 NA18964 0 0 2 2
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JA18953 NA18953 0 0 1 1
|
||||
JA18968 NA18968 0 0 2 2
|
||||
JA18959 NA18959 0 0 1 2
|
||||
JA18969 NA18969 0 0 2 1
|
||||
JA18960 NA18960 0 0 1 2
|
||||
JA18961 NA18961 0 0 1 2
|
||||
JA18972 NA18972 0 0 2 2
|
||||
JA18965 NA18965 0 0 1 2
|
||||
JA18973 NA18973 0 0 2 2
|
||||
JA18966 NA18966 0 0 1 2
|
||||
JA18975 NA18975 0 0 2 2
|
||||
JA18967 NA18967 0 0 1 2
|
||||
JA18976 NA18976 0 0 2 1
|
||||
JA18978 NA18978 0 0 2 2
|
||||
JA18970 NA18970 0 0 1 1
|
||||
JA18980 NA18980 0 0 2 2
|
||||
JA18995 NA18995 0 0 1 1
|
||||
JA18981 NA18981 0 0 2 2
|
||||
JA18971 NA18971 0 0 1 2
|
||||
JA18974 NA18974 0 0 1 1
|
||||
JA18987 NA18987 0 0 2 2
|
||||
JA18990 NA18990 0 0 1 1
|
||||
JA18991 NA18991 0 0 2 2
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||||
JA18994 NA18994 0 0 1 2
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JA18992 NA18992 0 0 2 2
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JA18997 NA18997 0 0 2 2
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||||
JA18998 NA18998 0 0 2 2
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JA19000 NA19000 0 0 1 2
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JA19005 NA19005 0 0 1 2
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JA18999 NA18999 0 0 2 2
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||||
JA19007 NA19007 0 0 1 2
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JA19003 NA19003 0 0 2 2
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JA19012 NA19012 0 0 1 2
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@@ -0,0 +1 @@
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l�����������������������οΎξΈ��όώΏ�ΏϋϊΏΏο/��ώ�ο―�κΈλκ°®Ύξ®γκΈ;μ/βοϊ―ο―ΞκΌοβ°―ώΟ�γ―ψ+μ?β�ϊ―ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ���ο�����Ί��ώ―ώοΏ�»��ώ���ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ�������ώο���ώ����ϋ�ϋ���»�ολ�ξΎ�Ίώ�ώ―ώοΏ�;ο?ώ���ολ�κΎ�Ίϊοώ―ξλΏώ;―>βοώ»
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@@ -0,0 +1,10 @@
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22 rs5992809 16.5965 16596539 0 C
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||||
22 rs12168131 16.6573 16657262 G A
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||||
22 rs390041 16.6629 16662916 T C
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||||
22 rs437633 16.6697 16669684 A G
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||||
22 rs450960 16.6909 16690858 T C
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||||
22 rs450975 16.6909 16690887 T C
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||||
22 rs451740 16.6912 16691174 T C
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||||
22 rs8139723 16.6917 16691696 T C
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||||
22 rs405490 16.6922 16692175 G A
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||||
22 rs415170 16.6935 16693517 G C
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@@ -0,0 +1,90 @@
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CH18526 NA18526 0 0 2 1
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||||
CH18524 NA18524 0 0 1 1
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||||
CH18529 NA18529 0 0 2 1
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||||
CH18558 NA18558 0 0 1 1
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||||
CH18532 NA18532 0 0 2 1
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||||
CH18561 NA18561 0 0 1 1
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||||
CH18562 NA18562 0 0 1 1
|
||||
CH18537 NA18537 0 0 2 2
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||||
CH18603 NA18603 0 0 1 2
|
||||
CH18540 NA18540 0 0 2 1
|
||||
CH18605 NA18605 0 0 1 1
|
||||
CH18542 NA18542 0 0 2 1
|
||||
CH18545 NA18545 0 0 2 1
|
||||
CH18572 NA18572 0 0 1 2
|
||||
CH18547 NA18547 0 0 2 2
|
||||
CH18609 NA18609 0 0 1 1
|
||||
CH18550 NA18550 0 0 2 1
|
||||
CH18608 NA18608 0 0 1 1
|
||||
CH18552 NA18552 0 0 2 1
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||||
CH18611 NA18611 0 0 1 1
|
||||
CH18555 NA18555 0 0 2 1
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||||
CH18564 NA18564 0 0 2 2
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CH18566 NA18566 0 0 2 1
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||||
CH18563 NA18563 0 0 1 1
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||||
CH18570 NA18570 0 0 2 1
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||||
CH18612 NA18612 0 0 1 2
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||||
CH18571 NA18571 0 0 2 1
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||||
CH18620 NA18620 0 0 1 1
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||||
CH18621 NA18621 0 0 1 1
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||||
CH18594 NA18594 0 0 2 1
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||||
CH18622 NA18622 0 0 1 2
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CH18573 NA18573 0 0 2 2
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||||
CH18623 NA18623 0 0 1 1
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||||
CH18576 NA18576 0 0 2 1
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||||
CH18577 NA18577 0 0 2 1
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||||
CH18624 NA18624 0 0 1 1
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||||
CH18579 NA18579 0 0 2 1
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||||
CH18632 NA18632 0 0 1 2
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||||
CH18582 NA18582 0 0 2 1
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||||
CH18633 NA18633 0 0 1 1
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||||
CH18635 NA18635 0 0 1 2
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||||
CH18592 NA18592 0 0 2 1
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||||
CH18636 NA18636 0 0 1 1
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||||
CH18593 NA18593 0 0 2 2
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||||
CH18637 NA18637 0 0 1 1
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||||
JA18942 NA18942 0 0 2 2
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||||
JA18940 NA18940 0 0 1 2
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||||
JA18951 NA18951 0 0 2 2
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||||
JA18943 NA18943 0 0 1 2
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JA18947 NA18947 0 0 2 2
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JA18944 NA18944 0 0 1 2
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||||
JA18945 NA18945 0 0 1 2
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||||
JA18949 NA18949 0 0 2 2
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||||
JA18948 NA18948 0 0 1 2
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||||
JA18952 NA18952 0 0 1 2
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||||
JA18956 NA18956 0 0 2 2
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||||
JA18964 NA18964 0 0 2 2
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||||
JA18953 NA18953 0 0 1 1
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||||
JA18968 NA18968 0 0 2 2
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||||
JA18959 NA18959 0 0 1 2
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||||
JA18969 NA18969 0 0 2 1
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||||
JA18960 NA18960 0 0 1 2
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||||
JA18961 NA18961 0 0 1 2
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JA18972 NA18972 0 0 2 2
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||||
JA18965 NA18965 0 0 1 2
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||||
JA18973 NA18973 0 0 2 2
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||||
JA18966 NA18966 0 0 1 2
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||||
JA18975 NA18975 0 0 2 2
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||||
JA18967 NA18967 0 0 1 2
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||||
JA18976 NA18976 0 0 2 1
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||||
JA18978 NA18978 0 0 2 2
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||||
JA18970 NA18970 0 0 1 1
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||||
JA18980 NA18980 0 0 2 2
|
||||
JA18995 NA18995 0 0 1 1
|
||||
JA18981 NA18981 0 0 2 2
|
||||
JA18971 NA18971 0 0 1 2
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||||
JA18974 NA18974 0 0 1 1
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||||
JA18987 NA18987 0 0 2 2
|
||||
JA18990 NA18990 0 0 1 1
|
||||
JA18991 NA18991 0 0 2 2
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||||
JA18994 NA18994 0 0 1 2
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||||
JA18992 NA18992 0 0 2 2
|
||||
JA18997 NA18997 0 0 2 2
|
||||
JA18998 NA18998 0 0 2 2
|
||||
JA19000 NA19000 0 0 1 2
|
||||
JA19005 NA19005 0 0 1 2
|
||||
JA18999 NA18999 0 0 2 2
|
||||
JA19007 NA19007 0 0 1 2
|
||||
JA19003 NA19003 0 0 2 2
|
||||
JA19012 NA19012 0 0 1 2
|
||||
@@ -0,0 +1,10 @@
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22 rs5992809 16.5965 16596539
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||||
22 rs12168131 16.6573 16657262
|
||||
22 rs390041 16.6629 16662916
|
||||
22 rs437633 16.6697 16669684
|
||||
22 rs450960 16.6909 16690858
|
||||
22 rs450975 16.6909 16690887
|
||||
22 rs451740 16.6912 16691174
|
||||
22 rs8139723 16.6917 16691696
|
||||
22 rs405490 16.6922 16692175
|
||||
22 rs415170 16.6935 16693517
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@@ -0,0 +1,90 @@
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CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C
|
||||
CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
|
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CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C
|
||||
CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C
|
||||
CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
|
||||
CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C
|
||||
CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C
|
||||
CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C
|
||||
CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C
|
||||
CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
|
||||
CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C
|
||||
CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C
|
||||
CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
|
||||
CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C
|
||||
CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C
|
||||
CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C
|
||||
CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C
|
||||
CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C
|
||||
CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C
|
||||
CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C
|
||||
CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C
|
||||
CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C
|
||||
CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
|
||||
CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
|
||||
CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C
|
||||
CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C
|
||||
CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C
|
||||
CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
|
||||
CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C
|
||||
CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C
|
||||
CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C
|
||||
CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C
|
||||
JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C
|
||||
JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
|
||||
JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C
|
||||
JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C
|
||||
JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C
|
||||
JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C
|
||||
JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C
|
||||
JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C
|
||||
JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C
|
||||
JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C
|
||||
JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C
|
||||
JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C
|
||||
JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C
|
||||
JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C
|
||||
JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G
|
||||
JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C
|
||||
JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C
|
||||
JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C
|
||||
JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C
|
||||
JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C
|
||||
JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C
|
||||
JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G
|
||||
JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C
|
||||
JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G
|
||||
JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C
|
||||
JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C
|
||||
JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C
|
||||
JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C
|
||||
JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C
|
||||
JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
|
||||
JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C
|
||||
JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
|
||||
JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
|
||||
JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C
|
||||
JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C
|
||||
@@ -83,7 +83,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.submit("runtool_btn")
|
||||
self.home()
|
||||
except AssertionError, err:
|
||||
errmsg = "The file (%s) doesn't exist." % filename
|
||||
errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename
|
||||
errmsg += str( err )
|
||||
raise AssertionError( errmsg )
|
||||
# Make sure every history item has a valid hid
|
||||
@@ -116,7 +116,36 @@ class TwillTestCase( unittest.TestCase ):
|
||||
raise AssertionError, "Invalid hid (%s) created when pasting %s" % ( hid, url_paste )
|
||||
# Wait for upload processing to finish (TODO: this should be done in each test case instead)
|
||||
self.wait()
|
||||
|
||||
def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', fam_file='', dbkey='unspecified (?)', base_name='rgenetics' ):
|
||||
"""Tests uploading either of 2 different composite data types ( lped and pbed )"""
|
||||
self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url )
|
||||
# Handle refresh_on_change
|
||||
self.refresh_form( "file_type", ftype )
|
||||
tc.fv( "1", "dbkey", dbkey )
|
||||
tc.fv( "1", "files_metadata|base_name", base_name )
|
||||
if ftype == 'lped':
|
||||
# lped data types include a ped_file and a map_file
|
||||
ped_file = self.get_filename( ped_file )
|
||||
tc.formfile( "1", "files_0|file_data", ped_file )
|
||||
map_file = self.get_filename( map_file )
|
||||
tc.formfile( "1", "files_1|file_data", map_file )
|
||||
elif ftype == 'pbed':
|
||||
# pbed data types include a bim_file, a bed_file and a fam_file
|
||||
bim_file = self.get_filename( bim_file )
|
||||
tc.formfile( "1", "files_0|file_data", bim_file )
|
||||
bed_file = self.get_filename( bed_file )
|
||||
tc.formfile( "1", "files_1|file_data", bed_file )
|
||||
fam_file = self.get_filename( fam_file )
|
||||
tc.formfile( "1", "files_2|file_data", fam_file )
|
||||
else:
|
||||
raise AssertionError, "Unsupported composite data type (%s) received, currently only lped and pbed data types are supported." % ftype
|
||||
tc.submit( "runtool_btn" )
|
||||
self.check_page_for_string( 'The following job has been succesfully added to the queue:' )
|
||||
check_str = 'Uploaded Composite Dataset (%s)' % ftype
|
||||
self.check_page_for_string( check_str )
|
||||
# Wait for upload processing to finish (TODO: this should be done in each test case instead)
|
||||
self.wait()
|
||||
self.check_history_for_string( check_str )
|
||||
# Functions associated with histories
|
||||
def check_history_for_errors( self ):
|
||||
"""Raises an exception if there are errors in a history"""
|
||||
@@ -522,7 +551,20 @@ class TwillTestCase( unittest.TestCase ):
|
||||
errmsg += str( err )
|
||||
raise AssertionError( errmsg )
|
||||
os.remove(temp_name)
|
||||
|
||||
def verify_composite_datatype_file_content( self, file_name, hda_id ):
|
||||
local_name = self.get_filename( file_name )
|
||||
temp_name = self.get_filename( 'temp_%s' % file_name )
|
||||
self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, hda_id, file_name ) )
|
||||
data = self.last_page()
|
||||
file( temp_name, 'wb' ).write( data )
|
||||
try:
|
||||
self.files_diff( local_name, temp_name )
|
||||
except AssertionError, err:
|
||||
os.remove( temp_name )
|
||||
errmsg = 'History item %s different than expected, difference:\n' % str( hda_id )
|
||||
errmsg += str( err )
|
||||
raise AssertionError( errmsg )
|
||||
os.remove( temp_name )
|
||||
def is_zipped( self, filename ):
|
||||
if not zipfile.is_zipfile( filename ):
|
||||
return False
|
||||
@@ -722,7 +764,29 @@ class TwillTestCase( unittest.TestCase ):
|
||||
# Add conditions for other control types here when necessary.
|
||||
pass
|
||||
tc.submit( button )
|
||||
|
||||
def refresh_form( self, control_name, value, form_no=0, **kwd ):
|
||||
"""Handles Galaxy's refresh_on_change for forms without ultimately submitting the form"""
|
||||
# control_name is the name of the form field that requires refresh_on_change, and value is
|
||||
# the value to which that field is being set.
|
||||
for i, f in enumerate( self.showforms() ):
|
||||
if i == form_no:
|
||||
break
|
||||
try:
|
||||
control = f.find_control( name=control_name )
|
||||
except:
|
||||
# This assumes we always want the first control of the given name, which may not be ideal...
|
||||
control = f.find_control( name=control_name, nr=0 )
|
||||
# Check for refresh_on_change attribute, submit a change if required
|
||||
if 'refresh_on_change' in control.attrs.keys():
|
||||
# Clear Control and set to proper value
|
||||
control.clear()
|
||||
tc.fv( f.name, control.name, value )
|
||||
# Create a new submit control, allows form to refresh, instead of going to next page
|
||||
control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} )
|
||||
control.add_to_form( f )
|
||||
control.fixup()
|
||||
# Submit for refresh
|
||||
tc.submit( '___refresh_grouping___' )
|
||||
def visit_page( self, page ):
|
||||
# tc.go("./%s" % page)
|
||||
if not page.startswith( "/" ):
|
||||
|
||||
@@ -45,6 +45,7 @@ class UploadData( TwillTestCase ):
|
||||
self.delete_history( id=self.security.encode_id( history1.id ) )
|
||||
def test_005_url_paste( self ):
|
||||
"""Test url paste behavior"""
|
||||
# Logged in as admin_user
|
||||
# Deleting the current history should have created a new history
|
||||
self.check_history_for_string( 'Your history is empty' )
|
||||
history2 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
|
||||
@@ -57,3 +58,38 @@ class UploadData( TwillTestCase ):
|
||||
self.check_history_for_string( 'Pasted Entry' )
|
||||
self.check_history_for_string( 'hello world' )
|
||||
self.delete_history( id=self.security.encode_id( history2.id ) )
|
||||
def test_010_upload_lped_composite_datatype_files( self ):
|
||||
"""Test uploading lped composite datatype files"""
|
||||
# Logged in as admin_user
|
||||
self.check_history_for_string( 'Your history is empty' )
|
||||
history3 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
|
||||
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
||||
.order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
|
||||
# lped data types include a ped_file and a map_file ( which is binary )
|
||||
self.upload_composite_datatype_file( 'lped', ped_file='tinywga.ped', map_file='tinywga.map', base_name='rgenetics' )
|
||||
# Get the latest hid for testing
|
||||
hda1 = galaxy.model.HistoryDatasetAssociation.query() \
|
||||
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
|
||||
assert hda1 is not None, "Problem retrieving hda1 from database"
|
||||
# We'll test against the resulting ped file and map file for correctness
|
||||
self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda1.id ) )
|
||||
self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda1.id ) )
|
||||
self.delete_history( id=self.security.encode_id( history3.id ) )
|
||||
def test_015_upload_pbed_composite_datatype_files( self ):
|
||||
"""Test uploading pbed composite datatype files"""
|
||||
# Logged in as admin_user
|
||||
self.check_history_for_string( 'Your history is empty' )
|
||||
history4 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
|
||||
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
||||
.order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
|
||||
# pbed data types include a bim_file, a bed_file and a fam_file
|
||||
self.upload_composite_datatype_file( 'pbed', bim_file='tinywga.bim', bed_file='tinywga.bed', fam_file='tinywga.fam', base_name='rgenetics' )
|
||||
# Get the latest hid for testing
|
||||
hda1 = galaxy.model.HistoryDatasetAssociation.query() \
|
||||
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
|
||||
assert hda1 is not None, "Problem retrieving hda1 from database"
|
||||
# We'll test against the resulting ped file and map file for correctness
|
||||
self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda1.id ) )
|
||||
self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda1.id ) )
|
||||
self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda1.id ) )
|
||||
self.delete_history( id=self.security.encode_id( history4.id ) )
|
||||
|
||||
Reference in New Issue
Block a user